diff --git a/README.md b/README.md new file mode 100644 index 00000000..e1085651 --- /dev/null +++ b/README.md @@ -0,0 +1,56 @@ +# Conformer-Rotamer Ensemble Sampling Tool + +[![Latest Version](https://img.shields.io/github/v/release/grimme-lab/crest)](https://github.com/grimme-lab/crest/releases/latest) +[![DOI](https://img.shields.io/badge/DOI-10.1039%2Fc9cp06869d%20-blue)](http://dx.doi.org/10.1039/c9cp06869d) + +This is the offical repository of the `crest` program developed by the Grimme group in Bonn. + +`crest` is an extension to the [`xtb`](https://github.com/grimme-lab/xtb) program. +It functions as an IO based OMP scheduler (*i.e.*, calculations are +performed by the `xtb` program) and tool for the creation and analysation of +structure ensembles. + +
+CREST +
+ +## Installation + +We are currently preparing the source code and will be providing it in this repository +with one of the upcoming releases. + +Until then please use the statically linked binaries (Intel Compiler 17.0.7) +that can be found at the [release page](https://github.com/grimme-lab/crest/releases), +of this repository. +Simply unpack the binary and add it to your *PATH* variable. +```bash +tar -xvzf crest.tgz +``` + +Also make sure that you have correctly installed and sourced the [`xtb`](https://github.com/grimme-lab/xtb) program before attempting any calculations with `crest`. + +## Examples + +This repository contains several examples for default applications of `crest`. + +See [`examples`](examples). To test the installation please try to run [example 0](examples/expl-0). + +## Documentation + +The `crest` documentation is hosted at [read-the-docs](https://xtb-docs.readthedocs.io/en/latest/crest.html). + +## Citations + +1. P. Pracht, F. Bohle, S. Grimme, *Phys. Chem. Chem. Phys.*, **2020**, 22, 7169-7192. + DOI: [10.1039/C9CP06869D](https://dx.doi.org/10.1039/C9CP06869D) + +2. S. Grimme, *J. Chem. Theory Comput.*, **2019**, 155, 2847-2862. + DOI: [10.1021/acs.jctc.9b00143](https://dx.doi.org/10.1021/acs.jctc.9b00143) + + +## License + +`crest` is distributed in the hope that it will be useful, +but without any warranty; without even the implied warranty of +merchantability or fitness for a particular purpose. + diff --git a/assets/crest.png b/assets/crest.png new file mode 100644 index 00000000..9f4fe152 Binary files /dev/null and b/assets/crest.png differ diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 00000000..36bd25ad --- /dev/null +++ b/examples/README.md @@ -0,0 +1,34 @@ +# Example applications of the CREST program + +This directory contains several examples for +standard applications of the `crest` program. + +Each example directory contains a input structure +(typically called `struc.xyz`) and a bash script +called `run.sh` that includes some information about +the example and will execute the calculation upon +execution. + +To run the example scripts simply go to the respective +directory and execute it from the command line: +```bash +./run.sh +``` + +It is assumed that the `xtb` and `crest` binaries +are present in the *PATH* variable as such. +The `run.sh` scripts will check for this, however. + + +## Examples + +0. *dry run* of the `crest` program +1. default conformational search (iMTD-GC) +2. example for different CMD settings +3. sorting an ensemble file (CREGEN) +4. constrained conformational sampling +5. standalone optimization along a trajectory +6. NCI sampling mode (iMTD-NCI) +7. protonation site sampling +8. modified protonation site sampling +9. tautomer sampling diff --git a/examples/expl-0/run.sh b/examples/expl-0/run.sh new file mode 100755 index 00000000..881b7737 --- /dev/null +++ b/examples/expl-0/run.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -dry + else + $crst struc.xyz -dry -xnam $xtbin + fi + +# Before starting any calculation, settings +# can be checked with the '-dry' flag. +# This will only print a summary about the +# selected settings and thresholds to the +# consol and check for the xtb binary. +# +# Every time the input file (struc.xyz) is +# something else than 'coord', a file called +# 'coord' will be (over-)written, containing +# the atomic coordinates in Bohr. CREST will +# then continue to use and overwrite this +# coord file for all further calculations. diff --git a/examples/expl-0/struc.xyz b/examples/expl-0/struc.xyz new file mode 100644 index 00000000..4297fe9a --- /dev/null +++ b/examples/expl-0/struc.xyz @@ -0,0 +1,14 @@ +12 + +C 1.00510 -0.04436 0.07729 +C 2.52196 -0.10014 0.05638 +C 3.03386 -1.52959 -0.04885 +O 4.45512 -1.53382 -0.04957 +H 0.66450 0.99293 0.15400 +H 0.60392 -0.59767 0.93240 +H 0.58435 -0.47325 -0.83778 +H 2.92490 0.36854 0.96213 +H 2.90338 0.49174 -0.78421 +H 2.68484 -2.01184 -0.96764 +H 2.69552 -2.12845 0.80244 +H 4.74911 -1.01511 -0.81774 diff --git a/examples/expl-1/run.sh b/examples/expl-1/run.sh new file mode 100755 index 00000000..015ccee7 --- /dev/null +++ b/examples/expl-1/run.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -ewin 2.0 + else + $crst struc.xyz -ewin 2.0 -xnam $xtbin + fi + + +# This will execute a conformational search with default settings +# for the 1-propanol molecule. +# The energy window is set to 2.0 kcal/mol with the '-ewin' flag +# (instead of the default 6.0 kcal/mol window) +# Within this window there should be 4 conformers for 1-propanol +# in the gas phase. +# The 4 unique conformers can be found in the file 'crest_conformers.xyz'. +# All degenerate conformers (rotamers, pseudo-enantiomers) of the 4 structures +# can be found in the file 'crest_rotamers.xyz' + + diff --git a/examples/expl-1/struc.xyz b/examples/expl-1/struc.xyz new file mode 100644 index 00000000..4297fe9a --- /dev/null +++ b/examples/expl-1/struc.xyz @@ -0,0 +1,14 @@ +12 + +C 1.00510 -0.04436 0.07729 +C 2.52196 -0.10014 0.05638 +C 3.03386 -1.52959 -0.04885 +O 4.45512 -1.53382 -0.04957 +H 0.66450 0.99293 0.15400 +H 0.60392 -0.59767 0.93240 +H 0.58435 -0.47325 -0.83778 +H 2.92490 0.36854 0.96213 +H 2.90338 0.49174 -0.78421 +H 2.68484 -2.01184 -0.96764 +H 2.69552 -2.12845 0.80244 +H 4.74911 -1.01511 -0.81774 diff --git a/examples/expl-2.5/run.sh b/examples/expl-2.5/run.sh new file mode 100755 index 00000000..2215a633 --- /dev/null +++ b/examples/expl-2.5/run.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -ewin 2.0 -quick -prop ohess + else + $crst struc.xyz -ewin 2.0 -quick -prop ohess -xnam $xtbin + fi + +# Some further calculations can be added automatically +# after the conformer search with the '-prop' command. +# In the above example, after searching for the +# conformers of 1-propanol, each conformer is optimized +# again and frequencies are calculated (ohess). +# The conformer ensemble is then re-ranked with free +# energies from RRHO contributions. +# +# There are also some different 'quick'-modes to run +# the conformational search with reduced settings. +# With these modes the conformational space will be +# explored less extensively, but it will speed up +# the calculation. ('-quick','-squick','-mquick') + diff --git a/examples/expl-2.5/struc.xyz b/examples/expl-2.5/struc.xyz new file mode 100644 index 00000000..4297fe9a --- /dev/null +++ b/examples/expl-2.5/struc.xyz @@ -0,0 +1,14 @@ +12 + +C 1.00510 -0.04436 0.07729 +C 2.52196 -0.10014 0.05638 +C 3.03386 -1.52959 -0.04885 +O 4.45512 -1.53382 -0.04957 +H 0.66450 0.99293 0.15400 +H 0.60392 -0.59767 0.93240 +H 0.58435 -0.47325 -0.83778 +H 2.92490 0.36854 0.96213 +H 2.90338 0.49174 -0.78421 +H 2.68484 -2.01184 -0.96764 +H 2.69552 -2.12845 0.80244 +H 4.74911 -1.01511 -0.81774 diff --git a/examples/expl-2/run.sh b/examples/expl-2/run.sh new file mode 100755 index 00000000..e2da43e9 --- /dev/null +++ b/examples/expl-2/run.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -ewin 2.0 -g h2o -gfn2 -T 4 + else + $crst struc.xyz -ewin 2.0 -g h2o -gfn2 -T 4 -xnam $xtbin + fi + + +# This will execute a conformational search with some manually changed +# settings for the 1-propanol molecule. +# The GBSA implicit solvation model for H2O is employed with the +# '-g' flag. +# Furthermore, the use of GFN2-xTB is requested explicitly ('-gfn2') +# and the program is ordered to use 4 CPU threads ('-T'). +# For a 1-propanol the conformers in implicit solvation are the +# same as in the gas phase, but the relative energies should +# differ significantly. +# Unique conformers can be found in the file 'crest_conformers.xyz'. +# All degenerate conformers (rotamers, pseudo-enantiomers) +# can be found in the file 'crest_rotamers.xyz' + + diff --git a/examples/expl-2/struc.xyz b/examples/expl-2/struc.xyz new file mode 100644 index 00000000..4297fe9a --- /dev/null +++ b/examples/expl-2/struc.xyz @@ -0,0 +1,14 @@ +12 + +C 1.00510 -0.04436 0.07729 +C 2.52196 -0.10014 0.05638 +C 3.03386 -1.52959 -0.04885 +O 4.45512 -1.53382 -0.04957 +H 0.66450 0.99293 0.15400 +H 0.60392 -0.59767 0.93240 +H 0.58435 -0.47325 -0.83778 +H 2.92490 0.36854 0.96213 +H 2.90338 0.49174 -0.78421 +H 2.68484 -2.01184 -0.96764 +H 2.69552 -2.12845 0.80244 +H 4.74911 -1.01511 -0.81774 diff --git a/examples/expl-3/run.sh b/examples/expl-3/run.sh new file mode 100755 index 00000000..00d10ba9 --- /dev/null +++ b/examples/expl-3/run.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +$crst struc.xyz -cregen xtb.trj -ewin 100.0 + + +# The sorting routine from the CREST conformational search can be +# used as a standalone to sort any .xyz or .trj ensemble file. +# The above command will sort the file xtb.trj according to +# its energy and determine duplicate structures. +# Two files are written analogous to 'crest_conformers.xyz' +# and 'crest_rotamers.xyz'. +# The new file 'crest_ensemble.xyz' will contain only unique +# structures from xtb.trj, while the new file 'xtb.trj.sorted' +# is just a sorted version of the original file (without the +# -ewin flag the default 6.0 kcal/mol window will be used) +# The routine requires a reference structure which is given +# by 'struc.xyz'. + diff --git a/examples/expl-3/struc.xyz b/examples/expl-3/struc.xyz new file mode 100644 index 00000000..38692b20 --- /dev/null +++ b/examples/expl-3/struc.xyz @@ -0,0 +1,14 @@ + 12 +FINAL HEAT OF FORMATION = -1.651323 + C 1.625257 -0.262628 -0.323273 + C 0.518221 0.706221 -0.335177 + C -0.859313 -0.005477 -0.327969 + H -1.683026 0.654493 -0.607965 + H -0.974493 -0.754480 -1.061658 + O -1.171503 -0.423846 1.012985 + H -0.837975 0.254126 1.683603 + H 0.615912 1.428650 0.457852 + H 0.597843 1.325129 -1.321583 + H 1.504113 -0.866659 0.564875 + H 2.639815 0.049302 -0.353007 + H 1.502315 -1.001480 -1.109649 diff --git a/examples/expl-3/xtb.trj b/examples/expl-3/xtb.trj new file mode 100644 index 00000000..3299a137 --- /dev/null +++ b/examples/expl-3/xtb.trj @@ -0,0 +1,700 @@ +12 + energy: -1.629564241025 gnorm: 0.000113350403 xtb: 6.2.2 (89a525f) !mtd1 +c 1.53648186970011 -0.56011339020012 0.12875854000020 +c 0.71156272809985 0.64005448549977 -0.29251203220000 +c -0.69209985700011 0.59004082799978 0.29706728279980 +h -0.64548898310024 0.58581159309989 1.39260758420008 +h -1.28389637169998 1.47157066540003 0.01629766849974 +o -1.40209608370006 -0.56855227450021 -0.08081479000000 +h -1.45086351409983 -0.63040405009998 -1.06227037799981 +h 1.21354305130004 1.57107642199978 0.00308663929983 +h 0.64019101169983 0.68031197700022 -1.38670739749992 +h 1.65321728849988 -0.59703079300021 1.21321138939994 +h 2.53623642799975 -0.54939098639996 -0.31107975810017 +h 1.05195720880020 -1.49082727710001 -0.17097349589985 +12 + energy: -1.642244239592 gnorm: 0.110638392028 xtb: 6.2.2 (89a525f) !mtd1 +c 1.77848006814652 -0.50202508937518 0.16020914741177 +c 0.70735637062331 0.65851564913335 -0.12731716824741 +c -0.70521061437189 0.39328384935263 0.34801994201362 +h -0.70155342713506 0.06941847609742 1.39206474968364 +h -1.18953642350702 1.43969958879376 0.36760733680604 +o -1.63520646733288 -0.42848568371421 -0.45427313297775 +h -1.81066902944799 -1.20337289776772 0.06629037843261 +h 1.05497293759682 1.58512313163768 0.31317456994293 +h 0.67076279748102 0.84644672717544 -1.23211171103949 +h 2.76199113102190 -0.10068914901133 0.31676161849241 +h 1.67463793894312 -1.27029751671006 -0.57195835010449 +h 1.63196019301442 -0.91068260920295 1.12694330997799 +12 + energy: -1.644095048085 gnorm: 0.131511503131 xtb: 6.2.2 (89a525f) !mtd1 +c 1.54887998028745 -0.45289018570871 0.02880374056948 +c 0.71220607971498 0.78864039075458 0.15181927864927 +c -0.79347606532435 0.39988837030191 0.36776974101614 +h -0.99568459781209 0.16307789856684 1.39075551334989 +h -1.49490278634342 1.30936020950559 0.09474510602642 +o -1.32980300696555 -0.66211167147448 -0.39957601922570 +h -1.21202841644358 -0.43581308726660 -1.31878936194789 +h 1.05483191678188 1.36692353719255 0.96725281722152 +h 0.92429429897284 1.38621899766339 -0.79749230467469 +h 1.11534504222332 -1.19499868227198 -0.73745758217582 +h 1.46808316953658 -1.02080965655843 1.02544481885686 +h 2.66926590950092 -0.36555778378638 -0.28903180301317 +12 + energy: -1.636001850071 gnorm: 0.135384383167 xtb: 6.2.2 (89a525f) !mtd1 +c 1.55684283807472 -0.43604264738953 0.05472612718237 +c 0.67903350905134 0.81156821859983 0.19476480629901 +c -0.80159733148271 0.26290989525318 0.43440644416264 +h -0.80096282979241 -0.33411850469276 1.25791569095988 +h -1.49283940482549 1.18708384938902 0.61889675996537 +o -1.22647444436850 -0.50697408025631 -0.66216318866890 +h -2.14373756207909 -0.81827937637993 -0.53725593376017 +h 1.13734651295643 1.39779299508074 0.95337682330965 +h 0.64892154492896 1.42850135727328 -0.76562760969880 +h 1.05110572281622 -1.35399993086980 0.25025887715415 +h 2.40727812490400 -0.41354508477786 0.70514067568230 +h 2.09565946434933 -0.54234800735009 -0.86041394107592 +12 + energy: -1.642064131398 gnorm: 0.120179100876 xtb: 6.2.2 (89a525f) !mtd1 +c 1.71711155082266 -0.38054362941784 0.06108490716577 +c 0.59213029271383 0.72817065165572 -0.09784509896926 +c -0.70599263942794 0.25908946260978 0.56533392399391 +h -0.46307009874333 -0.36165931571815 1.33263702568164 +h -1.31141343143456 1.16440810831158 0.93522031902891 +o -1.54097608708476 -0.49507059629021 -0.39567804555029 +h -1.09922416708471 -0.53487602234576 -1.29133661370419 +h 0.82887830182913 1.68454892147655 0.33051910246958 +h 0.46884176446393 0.79624122280223 -1.21199449995824 +h 2.22900973203302 -0.51544393330139 -0.88953399746242 +h 1.32749237638850 -1.36772708707401 0.33866444933253 +h 2.42344850640282 -0.21914477084228 0.87908934447352 +12 + energy: -1.641089136771 gnorm: 0.095868830445 xtb: 6.2.2 (89a525f) !mtd1 +c 1.52016626393876 -0.45865441198674 -0.13479000504689 +c 0.64458088237936 0.83907739968369 0.00309547591601 +c -0.76504753168159 0.49629006644297 0.39645129293914 +h -0.83968740706362 0.23970831992603 1.44147127373371 +h -1.52728977152449 1.28066394019180 0.05183390925138 +o -1.26480688815433 -0.66650536219474 -0.26247467568554 +h -1.24521518035707 -1.45291111771728 0.40255709897496 +h 1.17519490825928 1.47208173481835 0.74295905024731 +h 0.59756332798817 1.36352960068886 -0.96409469349109 +h 2.64274967209621 -0.29180491472283 0.04611205169302 +h 1.41181176931429 -0.80621563186458 -1.20437971454843 +h 1.20195442593307 -1.40870643331336 0.42553679500141 +12 + energy: -1.640963837819 gnorm: 0.096687388058 xtb: 6.2.2 (89a525f) !mtd1 +c 1.59315580484332 -0.33912173556364 -0.40697428718582 +c 0.68152993774592 0.62906046487905 0.39022411937856 +c -0.84536052637946 0.60007401835239 -0.03803623918729 +h -1.43396062508983 1.26014334444121 0.67684728067077 +h -1.00304501968801 1.00687787136294 -1.04771966117787 +o -1.36381473999190 -0.74889910936661 0.05621358820343 +h -0.97836039230615 -1.35638600819141 0.78327982231293 +h 0.72547179590667 0.38302529541933 1.52013092427705 +h 1.20583233254558 1.56982046990833 0.20371110350067 +h 2.29665087856527 0.08299582023580 -1.07244338974466 +h 0.97364209292663 -1.00977813406405 -0.89214804361074 +h 2.24497139950239 -0.96109725242286 0.13990076260898 +12 + energy: -1.637312165366 gnorm: 0.119745373326 xtb: 6.2.2 (89a525f) !mtd1 +c 1.91133594909067 -0.04913790365045 -0.54260345437376 +c 0.74680218994685 0.21639286893216 0.46924646202511 +c -0.72388119331819 0.29541813601404 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-0.54378171953048 -0.79240012684068 +c -0.83043829871890 -0.19182779238993 0.02529891962292 +h -1.22212993146340 0.78750591195937 -0.24237305059707 +h -1.63202614844494 -0.92387703573101 0.01424800704078 +o -0.46892362559414 -0.05324923005434 1.41785362298573 +h -1.26550933112521 -0.41513052121254 1.83506033136205 +h 0.03756365297269 -0.66285091942034 -1.81201601844770 +h 0.98867136108537 -1.43101730336540 -0.35493785556439 +h 2.18223509921988 0.64502660636832 -0.34980326681925 +h 0.67813056473857 1.20951133414142 0.18740214504569 +h 1.12969054737438 1.34951107139674 -1.56727438985830 +12 + energy: -1.647035616221 gnorm: 0.081342362207 xtb: 6.2.2 (89a525f) !mtd1 +c 1.29706441549241 0.72319722188022 -0.59203995881183 +c 0.39575630984126 -0.54426483762175 -0.73411873991835 +c -0.86457334075739 -0.23495851609211 0.00569539470345 +h -1.44356006209983 0.56084048172586 -0.53067142836337 +h -1.40134505274833 -1.21481255216610 -0.04809278073350 +o -0.73743789546605 0.06990776194417 1.37466914886691 +h -0.13946117577377 -0.51962440616299 1.90818304736510 +h 0.16122603261523 -0.75707710036079 -1.78613567391846 +h 0.97030425028258 -1.34427213796623 -0.28930980943073 +h 1.99813011819941 0.86425284009363 -1.46549943292867 +h 1.80638265102311 0.91595103833180 0.38962246992746 +h 0.67839086237109 1.60144346691619 -0.81293431262838 +12 + energy: -1.636385266477 gnorm: 0.080849379348 xtb: 6.2.2 (89a525f) !mtd1 +c 1.39867228749153 0.71439371413643 -0.61686186587722 +c 0.32139623821506 -0.34539588929124 -0.75741803301922 +c -0.97158260061882 -0.43198192230077 0.05795864671708 +h -1.89739850618403 -0.09239223288863 -0.39621959533756 +h -1.12298532790841 -1.51127079836366 0.20741548941578 +o -0.70098425332805 0.14674624250896 1.35520900495802 +h -0.24742064662037 -0.46477080276208 2.02335689939414 +h 0.14033543721930 -0.21596862460299 -1.85601255540714 +h 0.79746090917188 -1.33467142002625 -0.65322492286890 +h 2.42900621780179 0.38564067230763 -0.79524704661906 +h 1.36682598173388 1.24450299701426 0.30468419698734 +h 1.35162218042564 1.52273200147950 -1.33878957058677 diff --git a/examples/expl-4/run.sh b/examples/expl-4/run.sh new file mode 100755 index 00000000..7f62e3c2 --- /dev/null +++ b/examples/expl-4/run.sh @@ -0,0 +1,32 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -constrain 1-4 + $crst struc.xyz -cinp .xcontrol.sample + else + $crst struc.xyz -constrain 1-4 + $crst struc.xyz -cinp .xcontorl.sample -xnam $xtbin + fi + + +# Constraint conformational sampling is possible by +# providing the constrainment info as a file +# via the '-cinp' flag. +# For detailed information about the constraining +# options see the online documentation of +# CREST and xTB. +# However, a dummy constraining file '.xcontrol.sample' +# can be written by CREST with a seperate call using +# The '-constrain ' flag. +# In the above example the carbon atoms and the oxygen +# atom of 1-propanol (atoms 1-4) will be constrained. +# In the resulting "ensemble" only conformers resulting +# from different OH dihedral angles will be present +# (2 conformers total) diff --git a/examples/expl-4/struc.xyz b/examples/expl-4/struc.xyz new file mode 100644 index 00000000..4297fe9a --- /dev/null +++ b/examples/expl-4/struc.xyz @@ -0,0 +1,14 @@ +12 + +C 1.00510 -0.04436 0.07729 +C 2.52196 -0.10014 0.05638 +C 3.03386 -1.52959 -0.04885 +O 4.45512 -1.53382 -0.04957 +H 0.66450 0.99293 0.15400 +H 0.60392 -0.59767 0.93240 +H 0.58435 -0.47325 -0.83778 +H 2.92490 0.36854 0.96213 +H 2.90338 0.49174 -0.78421 +H 2.68484 -2.01184 -0.96764 +H 2.69552 -2.12845 0.80244 +H 4.74911 -1.01511 -0.81774 diff --git a/examples/expl-5/run.sh b/examples/expl-5/run.sh new file mode 100755 index 00000000..f9a722ac --- /dev/null +++ b/examples/expl-5/run.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst -mdopt xtb.trj + else + $crst -mdopt xtb.trj -xnam $xtbin + fi + + +# A ensemble file (or MD trajectory) can also +# be optimized in a standalone application +# of CREST using the '-mdopt' flag. +# The optimized structures are written to a +# file called 'crest_ensemble.xyz', but will +# not be sorted in any way. diff --git a/examples/expl-5/xtb.trj b/examples/expl-5/xtb.trj new file mode 100644 index 00000000..3299a137 --- /dev/null +++ b/examples/expl-5/xtb.trj @@ -0,0 +1,700 @@ +12 + energy: -1.629564241025 gnorm: 0.000113350403 xtb: 6.2.2 (89a525f) !mtd1 +c 1.53648186970011 -0.56011339020012 0.12875854000020 +c 0.71156272809985 0.64005448549977 -0.29251203220000 +c -0.69209985700011 0.59004082799978 0.29706728279980 +h -0.64548898310024 0.58581159309989 1.39260758420008 +h -1.28389637169998 1.47157066540003 0.01629766849974 +o -1.40209608370006 -0.56855227450021 -0.08081479000000 +h -1.45086351409983 -0.63040405009998 -1.06227037799981 +h 1.21354305130004 1.57107642199978 0.00308663929983 +h 0.64019101169983 0.68031197700022 -1.38670739749992 +h 1.65321728849988 -0.59703079300021 1.21321138939994 +h 2.53623642799975 -0.54939098639996 -0.31107975810017 +h 1.05195720880020 -1.49082727710001 -0.17097349589985 +12 + energy: -1.642244239592 gnorm: 0.110638392028 xtb: 6.2.2 (89a525f) !mtd1 +c 1.77848006814652 -0.50202508937518 0.16020914741177 +c 0.70735637062331 0.65851564913335 -0.12731716824741 +c -0.70521061437189 0.39328384935263 0.34801994201362 +h -0.70155342713506 0.06941847609742 1.39206474968364 +h -1.18953642350702 1.43969958879376 0.36760733680604 +o -1.63520646733288 -0.42848568371421 -0.45427313297775 +h -1.81066902944799 -1.20337289776772 0.06629037843261 +h 1.05497293759682 1.58512313163768 0.31317456994293 +h 0.67076279748102 0.84644672717544 -1.23211171103949 +h 2.76199113102190 -0.10068914901133 0.31676161849241 +h 1.67463793894312 -1.27029751671006 -0.57195835010449 +h 1.63196019301442 -0.91068260920295 1.12694330997799 +12 + energy: -1.644095048085 gnorm: 0.131511503131 xtb: 6.2.2 (89a525f) !mtd1 +c 1.54887998028745 -0.45289018570871 0.02880374056948 +c 0.71220607971498 0.78864039075458 0.15181927864927 +c -0.79347606532435 0.39988837030191 0.36776974101614 +h -0.99568459781209 0.16307789856684 1.39075551334989 +h -1.49490278634342 1.30936020950559 0.09474510602642 +o -1.32980300696555 -0.66211167147448 -0.39957601922570 +h -1.21202841644358 -0.43581308726660 -1.31878936194789 +h 1.05483191678188 1.36692353719255 0.96725281722152 +h 0.92429429897284 1.38621899766339 -0.79749230467469 +h 1.11534504222332 -1.19499868227198 -0.73745758217582 +h 1.46808316953658 -1.02080965655843 1.02544481885686 +h 2.66926590950092 -0.36555778378638 -0.28903180301317 +12 + energy: -1.636001850071 gnorm: 0.135384383167 xtb: 6.2.2 (89a525f) !mtd1 +c 1.55684283807472 -0.43604264738953 0.05472612718237 +c 0.67903350905134 0.81156821859983 0.19476480629901 +c -0.80159733148271 0.26290989525318 0.43440644416264 +h -0.80096282979241 -0.33411850469276 1.25791569095988 +h -1.49283940482549 1.18708384938902 0.61889675996537 +o -1.22647444436850 -0.50697408025631 -0.66216318866890 +h -2.14373756207909 -0.81827937637993 -0.53725593376017 +h 1.13734651295643 1.39779299508074 0.95337682330965 +h 0.64892154492896 1.42850135727328 -0.76562760969880 +h 1.05110572281622 -1.35399993086980 0.25025887715415 +h 2.40727812490400 -0.41354508477786 0.70514067568230 +h 2.09565946434933 -0.54234800735009 -0.86041394107592 +12 + energy: -1.642064131398 gnorm: 0.120179100876 xtb: 6.2.2 (89a525f) !mtd1 +c 1.71711155082266 -0.38054362941784 0.06108490716577 +c 0.59213029271383 0.72817065165572 -0.09784509896926 +c -0.70599263942794 0.25908946260978 0.56533392399391 +h -0.46307009874333 -0.36165931571815 1.33263702568164 +h -1.31141343143456 1.16440810831158 0.93522031902891 +o -1.54097608708476 -0.49507059629021 -0.39567804555029 +h -1.09922416708471 -0.53487602234576 -1.29133661370419 +h 0.82887830182913 1.68454892147655 0.33051910246958 +h 0.46884176446393 0.79624122280223 -1.21199449995824 +h 2.22900973203302 -0.51544393330139 -0.88953399746242 +h 1.32749237638850 -1.36772708707401 0.33866444933253 +h 2.42344850640282 -0.21914477084228 0.87908934447352 +12 + energy: -1.641089136771 gnorm: 0.095868830445 xtb: 6.2.2 (89a525f) !mtd1 +c 1.52016626393876 -0.45865441198674 -0.13479000504689 +c 0.64458088237936 0.83907739968369 0.00309547591601 +c -0.76504753168159 0.49629006644297 0.39645129293914 +h -0.83968740706362 0.23970831992603 1.44147127373371 +h -1.52728977152449 1.28066394019180 0.05183390925138 +o -1.26480688815433 -0.66650536219474 -0.26247467568554 +h -1.24521518035707 -1.45291111771728 0.40255709897496 +h 1.17519490825928 1.47208173481835 0.74295905024731 +h 0.59756332798817 1.36352960068886 -0.96409469349109 +h 2.64274967209621 -0.29180491472283 0.04611205169302 +h 1.41181176931429 -0.80621563186458 -1.20437971454843 +h 1.20195442593307 -1.40870643331336 0.42553679500141 +12 + energy: -1.640963837819 gnorm: 0.096687388058 xtb: 6.2.2 (89a525f) !mtd1 +c 1.59315580484332 -0.33912173556364 -0.40697428718582 +c 0.68152993774592 0.62906046487905 0.39022411937856 +c -0.84536052637946 0.60007401835239 -0.03803623918729 +h -1.43396062508983 1.26014334444121 0.67684728067077 +h -1.00304501968801 1.00687787136294 -1.04771966117787 +o -1.36381473999190 -0.74889910936661 0.05621358820343 +h -0.97836039230615 -1.35638600819141 0.78327982231293 +h 0.72547179590667 0.38302529541933 1.52013092427705 +h 1.20583233254558 1.56982046990833 0.20371110350067 +h 2.29665087856527 0.08299582023580 -1.07244338974466 +h 0.97364209292663 -1.00977813406405 -0.89214804361074 +h 2.24497139950239 -0.96109725242286 0.13990076260898 +12 + energy: -1.637312165366 gnorm: 0.119745373326 xtb: 6.2.2 (89a525f) !mtd1 +c 1.91133594909067 -0.04913790365045 -0.54260345437376 +c 0.74680218994685 0.21639286893216 0.46924646202511 +c -0.72388119331819 0.29541813601404 -0.19333602638614 +h -1.09722815744165 1.34448971031285 0.03710595653177 +h -0.68409893981535 0.17282787503416 -1.22229661787256 +o -1.78745136645095 -0.50385242439524 0.31009821996485 +h -2.20549355159232 -0.17982943238300 1.13553295375473 +h 0.78755602146423 -0.72122624810652 1.12449652733763 +h 0.83202755662025 1.09258068630994 1.07863563581287 +h 1.65931566571358 0.47884015903745 -1.48875776510552 +h 2.22420335704199 -1.09235029383224 -0.79525306041132 +h 2.87158664786781 0.48630019782342 -0.31632916993057 +12 + energy: -1.640073986761 gnorm: 0.143550137017 xtb: 6.2.2 (89a525f) !mtd1 +c 1.98567504289686 0.34686642920142 -0.43410181975397 +c 0.69029419446237 -0.19118598544302 0.34522728277633 +c -0.74786302784654 -0.15377596233465 -0.37054179760724 +h -0.84458542551695 0.73717818914931 -1.07894332855616 +h -0.88169960394728 -0.96267534154318 -0.96630077841112 +o -1.88155379577552 -0.05999474395143 0.51661140989505 +h -1.62133348028701 0.47368262657921 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-0.79524704661906 +h 1.36682598173388 1.24450299701426 0.30468419698734 +h 1.35162218042564 1.52273200147950 -1.33878957058677 diff --git a/examples/expl-6/run.sh b/examples/expl-6/run.sh new file mode 100755 index 00000000..d507701b --- /dev/null +++ b/examples/expl-6/run.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -nci + else + $crst struc.xyz -nci -xnam $xtbin + fi + + +# This will execute the NCI sampling mode of CREST of the +# water trimer with default settings. +# A wall-potential is automatically generated and added to +# the calculation to prevent dissociation. +# The NCI mode is a special case of the constrained sampling. +# Just like the regular conformational search unique conformers +# can be found in the file 'crest_conformers.xyz'. +# All degenerate conformers (rotamers, pseudo-enantiomers) +# can be found in the file 'crest_rotamers.xyz' + + diff --git a/examples/expl-6/struc.xyz b/examples/expl-6/struc.xyz new file mode 100644 index 00000000..5553af95 --- /dev/null +++ b/examples/expl-6/struc.xyz @@ -0,0 +1,11 @@ + 9 +FINAL HEAT OF FORMATION = 0.000000 + H -1.091354 2.083948 0.561412 + O -0.873213 1.360333 -0.037725 + H -1.126153 -0.540943 0.037240 + H 0.094609 1.245770 0.037306 + O 1.614744 0.076014 -0.037729 + O -0.741528 -1.436357 -0.037711 + H -1.259101 -1.987119 0.561339 + H 2.350402 -0.096756 0.561513 + H 1.031565 -0.704748 0.037192 diff --git a/examples/expl-7/run.sh b/examples/expl-7/run.sh new file mode 100755 index 00000000..d1341045 --- /dev/null +++ b/examples/expl-7/run.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -protonate + else + $crst struc.xyz -protonate -xnam $xtbin + fi + + +# This command will create protomers of the uracil molecule. +# The default energy window for this application is 30 kcal/mol +# Only 3 structures should remain in the gas phase at the +# default GFN2-xTB level. +# The structures can be found in the file 'protonated.xyz' diff --git a/examples/expl-7/struc.xyz b/examples/expl-7/struc.xyz new file mode 100644 index 00000000..73524a28 --- /dev/null +++ b/examples/expl-7/struc.xyz @@ -0,0 +1,14 @@ +12 + energy: -24.614946947602 gnorm: 0.000456827525 xtb: 6.2.2 (89a525f) +O 1.01382029544030 0.03880681993718 0.26260657568622 +C 2.21194959420030 0.00777551853774 0.13894624850894 +N 2.97633014247497 1.15928881874167 0.06760158128732 +C 4.33128423994495 1.14641376546424 -0.07421492522129 +C 5.02090106234646 -0.00303350704424 -0.15435476958224 +C 4.32754207903802 -1.27903972647711 -0.09166688984675 +O 4.83244816077160 -2.37420082989590 -0.15422059425404 +N 2.94450163810970 -1.14763022456257 0.05629094590508 +H 2.46829084494664 2.03038084438831 0.12488082938105 +H 4.81038312241915 2.11362921965719 -0.11757996835012 +H 6.09011013882395 -0.02137897779485 -0.26646726330202 +H 2.41547828301905 -2.01176145142300 0.10488837035251 diff --git a/examples/expl-8/run.sh b/examples/expl-8/run.sh new file mode 100755 index 00000000..d28b597c --- /dev/null +++ b/examples/expl-8/run.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -protonate -swel Cs+ + else + $crst struc.xyz -protonate -swel Cs+ -xnam $xtbin + fi + +# In a modified version of the protonation tool +# other ionization adducts can be created +# (only mono nuclear ions) +# To do this, the flag '-swel' (short for switch element) +# is used to indicate the new ion and its charge, +# e.g., Na+, Ca2+, Li+, etc. +# +# As a example the alpha-D-glucose-Cs+ adducts +# will be created at the GFN2-xTB level with the above command. +# The adducts can be found in the file 'protonated.xyz' + diff --git a/examples/expl-8/struc.xyz b/examples/expl-8/struc.xyz new file mode 100644 index 00000000..a3c58227 --- /dev/null +++ b/examples/expl-8/struc.xyz @@ -0,0 +1,26 @@ + 24 +FINAL HEAT OF FORMATION = 0.000000 + O -1.240000 0.500286 0.389534 + O -3.422179 -1.988021 -1.200876 + O -1.030343 -2.500198 1.371244 + O -0.269585 -1.376682 -2.050459 + O 0.714096 0.825174 -0.948699 + O -4.564244 0.596025 -1.237038 + C -2.604750 -1.434635 -0.186435 + C -1.275745 -2.232516 0.002738 + C -2.309462 0.069148 -0.458819 + C -0.090913 -1.462394 -0.648941 + C 0.038626 -0.020969 -0.037264 + C -3.562580 0.927621 -0.299600 + H -3.175049 -1.514611 0.751562 + H -1.394054 -3.206789 -0.495459 + H -1.941229 0.164323 -1.490086 + H 0.840456 -2.024192 -0.479114 + H 0.639496 -0.057270 0.885117 + H -3.985456 0.780616 0.699514 + H -3.317920 1.993716 -0.382206 + H -4.113958 -1.329897 -1.403262 + H -1.021769 -1.655987 1.868817 + H 0.187245 -0.582574 -2.396515 + H 1.659435 0.569359 -1.034662 + H -4.311180 0.903728 -2.134995 diff --git a/examples/expl-9/run.sh b/examples/expl-9/run.sh new file mode 100755 index 00000000..a487ef16 --- /dev/null +++ b/examples/expl-9/run.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +xtbin='xtb' +crst='crest' + +command -v $xtbin >/dev/null 2>&1 || { echo >&2 "Cannot find xtb binary. Exit."; exit 1; } +command -v $crst >/dev/null 2>&1 || { echo >&2 "Cannot find crest binary. Exit."; exit 1; } + +if [ $xtbin == 'xtb' ] + then + $crst struc.xyz -tautomerize -ewin 10.0 + else + $crst struc.xyz -tautomerize -ewin 10.0 -xnam $xtbin + fi + +# The -tautomerize flag can be used to request +# a screening of prototropic tautomers. +# The structures are build from a sequence of +# protonating and deprotonating steps of the +# (neutral) input structure. +# In the above example this procedure is +# performed on the guanine molecule to get +# the gas phase tautomers at GFN2-xTB level. +# Within the 10 kcal/mol window 5 tautomers +# should remain at this level. +# The structures can be found in 'tautomers.xyz'. + diff --git a/examples/expl-9/struc.xyz b/examples/expl-9/struc.xyz new file mode 100644 index 00000000..725a04d3 --- /dev/null +++ b/examples/expl-9/struc.xyz @@ -0,0 +1,18 @@ +16 + energy: -31.983681788270 gnorm: 0.000372144832 xtb: 6.2.2 (89a525f) +N 1.46226284012671 0.18335744247169 -0.07855270314916 +C 1.31781205014203 -1.15293393777405 0.05955064599303 +C 1.54055132778996 -2.13428714261960 -0.91007075980005 +C 1.98029754954570 -1.74761862944617 -2.21865239727883 +N 2.10914370306048 -0.33402358897783 -2.27674973147307 +C 1.86775867472018 0.54390043382692 -1.26343764079100 +N 1.27680953207984 -3.36757233307534 -0.37748854905490 +C 0.91461226786592 -3.14740906594264 0.84460715972356 +N 0.91768716624572 -1.81594469141732 1.17440471889163 +O 2.23471850070944 -2.39670706107528 -3.20454497820690 +N 2.11460025487082 1.85836120568312 -1.49845077783225 +H 0.67952040591559 -1.39514835256529 2.05664466916869 +H 0.63659476510547 -3.91144927326480 1.54245387480526 +H 2.43918920019300 0.01672894983906 -3.16809193535854 +H 1.78950116764777 2.49655065642122 -0.79277065540295 +H 2.15173216814906 2.19392916334893 -2.44513710915798