[gmx-users] amide-capped C-terminus; OPLS force field
Dear all, Does anyone have any experience with capping C-terminal amino acid residues in the OPLS force field? What atomtypes should I use to maintain neutrality of the system? eg. If i have a cystine at the C-terminus residue, and I use the following atomtypes N opls_238 -0.5 H opls_241 0.3 CAopls_224B 0.14 HAopls_140 0.06 CBopls_214 0.0975 HB1 opls_140 0.06 HB2 opls_140 0.06 SGopls_203 -0.2175 C opls_2350.5 O opls_236 -0.5 NTopls_900 -0.9 H1opls_909 0.36 H2opls_909 0.36 The system has a -0.18 qtotal (overall charge). Any help is appreciated. Regards, Sahil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Two atom oscillational period less than the time step
Dear GMX users, Hello, I would like to discuss the grompp message that tells the bonded atoms oscillational period less than 10 times the time step. I am using 0.002 ps time step. The simulation was stopped because of LINCS warming. Is it need to decrease time step at least 10 times? Instead of this, can I remove constraint and use the 0.0005 ps time step? On the other hand, after long equilibration with 0.0001 time step, can I increase the time step until 0.001? How can I solve this problem? If you have any experience, please let me advice. Thank you. Regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue
For the error: ``` ^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446: 467.9 M-cycles ^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372: 451.4 M-cycles /var/spool/slurmd/job2321134/slurm_script: line 44: 29866 Segmentation fault gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu -ntomp 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS -cpt 60 -cpi -noappend ``` I got these driver info: ``` GROMACS: gmx mdrun, version 2019.4 Executable: /home/rsexton2/Library/gromacs/2019.4/test1/bin/gmx Data prefix: /home/rsexton2/Library/gromacs/2019.4/test1 Working dir: /scratch/czhan178/project/NapA-2019.4/gromacs_test_1/test_9 Process ID: 29866 Command line: gmx mdrun -v -s md_seed_fixed.tpr -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu -ntomp 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh 2 -cpt 60 -cpi -noappend GROMACS version:2019.4 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:CUDA SIMD instructions: AVX2_256 FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG support:enabled Hwloc support: hwloc-1.11.2 Tracing support:disabled C compiler: /packages/7x/gcc/gcc-7.3.0/bin/gcc GNU 7.3.0 C compiler flags:-mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /packages/7x/gcc/gcc-7.3.0/bin/g++ GNU 7.3.0 C++ compiler flags: -mavx2 -mfma-std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /packages/7x/cuda/9.2.88.1/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Wed_Apr_11_23:16:29_CDT_2018;Cuda compilation tools, release 9.2, V9.2.88 CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;;; ;-mavx2;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver:9.20 CUDA runtime: 9.20 ``` I'll run -notunepme option and get you updated. Chenou On Mon, Dec 2, 2019 at 2:13 PM Mark Abraham wrote: > Hi, > > What driver version is reported in the respective log files? Does the error > persist if mdrun -notunepme is used? > > Mark > > On Mon., 2 Dec. 2019, 21:18 Chenou Zhang, wrote: > > > Hi Gromacs developers, > > > > I'm currently running gromacs 2019.4 on our university's HPC cluster. To > > fully utilize the GPU nodes, I followed notes on > > > > > http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html > > . > > > > > > And here is the command I used for my runs. > > ``` > > gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu > -ntomp > > 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS -cpt 60 > -cpi > > -noappend > > ``` > > > > And for some of those runs, they might fail with the following error: > > ``` > > --- > > > > Program: gmx mdrun, version 2019.4 > > > > Source file: src/gromacs/gpu_utils/cudautils.cuh (line 229) > > > > MPI rank:3 (out of 8) > > > > > > > > Fatal error: > > > > cudaStreamSynchronize failed: an illegal memory access was encountered > > > > > > > > For more information and tips for troubleshooting, please check the > GROMACS > > > > website at http://www.gromacs.org/Documentation/Errors > > ``` > > > > we also had a different error from slurm system: > > ``` > > ^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446: 467.9 > > M-cycles > > ^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372: 451.4 > > M-cycles > > /var/spool/slurmd/job2321134/slurm_script: line 44: 29866 Segmentation > > fault gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on > -nb > > gpu -ntomp 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS > > -cpt 60 -cpi -noappend > > ``` > > > > We first thought this could due to compiler issue and tried different > > settings as following: > > ===test1=== > > > > module load cuda/9.2.88.1 > > module load gcc/7.3.0 > > . /home/rsexton2/Library/gromacs/2019.4/test1/bin/GMXRC > > > > ===test2=== > > > > module load cuda/9.2.88.1 > > module load gcc/6x > > . /home/rsexton2/Library/gromacs/2019.4/test2/bin/GMXRC > > > > ===test3=== > > > > module load cuda/9.2.148 > > module load gcc/7.3.0 > > . /home/rsexton2/Library/gromacs/2019.4/test3/bin/GMXRC > > > > ===test4=== > > > > module load cuda/9.2.148 > > module load gcc/6x > > . /home/rsexton2/Library/gromacs/2019.4/test4/bin/GMXRC > > > > ===test5=== > > > > module load cuda/9.1.85 > > module load
Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue
Hi, What driver version is reported in the respective log files? Does the error persist if mdrun -notunepme is used? Mark On Mon., 2 Dec. 2019, 21:18 Chenou Zhang, wrote: > Hi Gromacs developers, > > I'm currently running gromacs 2019.4 on our university's HPC cluster. To > fully utilize the GPU nodes, I followed notes on > > http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html > . > > > And here is the command I used for my runs. > ``` > gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu -ntomp > 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS -cpt 60 -cpi > -noappend > ``` > > And for some of those runs, they might fail with the following error: > ``` > --- > > Program: gmx mdrun, version 2019.4 > > Source file: src/gromacs/gpu_utils/cudautils.cuh (line 229) > > MPI rank:3 (out of 8) > > > > Fatal error: > > cudaStreamSynchronize failed: an illegal memory access was encountered > > > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > ``` > > we also had a different error from slurm system: > ``` > ^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446: 467.9 > M-cycles > ^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372: 451.4 > M-cycles > /var/spool/slurmd/job2321134/slurm_script: line 44: 29866 Segmentation > fault gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb > gpu -ntomp 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS > -cpt 60 -cpi -noappend > ``` > > We first thought this could due to compiler issue and tried different > settings as following: > ===test1=== > > module load cuda/9.2.88.1 > module load gcc/7.3.0 > . /home/rsexton2/Library/gromacs/2019.4/test1/bin/GMXRC > > ===test2=== > > module load cuda/9.2.88.1 > module load gcc/6x > . /home/rsexton2/Library/gromacs/2019.4/test2/bin/GMXRC > > ===test3=== > > module load cuda/9.2.148 > module load gcc/7.3.0 > . /home/rsexton2/Library/gromacs/2019.4/test3/bin/GMXRC > > ===test4=== > > module load cuda/9.2.148 > module load gcc/6x > . /home/rsexton2/Library/gromacs/2019.4/test4/bin/GMXRC > > ===test5=== > > module load cuda/9.1.85 > module load gcc/6x > . /home/rsexton2/Library/gromacs/2019.4/test5/bin/GMXRC > > ===test6=== > > module load cuda/9.0.176 > module load gcc/6x > . /home/rsexton2/Library/gromacs/2019.4/test6/bin/GMXRC > > ===test7=== > > module load cuda/9.2.88.1 > module load gccgpu/7.4.0 > . /home/rsexton2/Library/gromacs/2019.4/test7/bin/GMXRC > > > However we still ended up with the same errors showed above. Does anyone > know where does the cudaStreamSynchronize come in? Or am I wrongly using > those gmx gpu commands? > > Any input will be appreciated! > > Thanks! > Chenou > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue
Hi Gromacs developers, I'm currently running gromacs 2019.4 on our university's HPC cluster. To fully utilize the GPU nodes, I followed notes on http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html. And here is the command I used for my runs. ``` gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu -ntomp 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS -cpt 60 -cpi -noappend ``` And for some of those runs, they might fail with the following error: ``` --- Program: gmx mdrun, version 2019.4 Source file: src/gromacs/gpu_utils/cudautils.cuh (line 229) MPI rank:3 (out of 8) Fatal error: cudaStreamSynchronize failed: an illegal memory access was encountered For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ``` we also had a different error from slurm system: ``` ^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446: 467.9 M-cycles ^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372: 451.4 M-cycles /var/spool/slurmd/job2321134/slurm_script: line 44: 29866 Segmentation fault gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu -ntomp 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS -cpt 60 -cpi -noappend ``` We first thought this could due to compiler issue and tried different settings as following: ===test1=== module load cuda/9.2.88.1 module load gcc/7.3.0 . /home/rsexton2/Library/gromacs/2019.4/test1/bin/GMXRC ===test2=== module load cuda/9.2.88.1 module load gcc/6x . /home/rsexton2/Library/gromacs/2019.4/test2/bin/GMXRC ===test3=== module load cuda/9.2.148 module load gcc/7.3.0 . /home/rsexton2/Library/gromacs/2019.4/test3/bin/GMXRC ===test4=== module load cuda/9.2.148 module load gcc/6x . /home/rsexton2/Library/gromacs/2019.4/test4/bin/GMXRC ===test5=== module load cuda/9.1.85 module load gcc/6x . /home/rsexton2/Library/gromacs/2019.4/test5/bin/GMXRC ===test6=== module load cuda/9.0.176 module load gcc/6x . /home/rsexton2/Library/gromacs/2019.4/test6/bin/GMXRC ===test7=== module load cuda/9.2.88.1 module load gccgpu/7.4.0 . /home/rsexton2/Library/gromacs/2019.4/test7/bin/GMXRC However we still ended up with the same errors showed above. Does anyone know where does the cudaStreamSynchronize come in? Or am I wrongly using those gmx gpu commands? Any input will be appreciated! Thanks! Chenou -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] toluene as a slovent
You also require a topology file for the toluene (.itp), include that in the system topology file (.top): *#include "toluene.itp" * Then add the molecule name and number of molecules added to the system to the molecule section at the end of the system topology file: [ molecules ]Toluene254 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 2 Dec 2019 at 19:44, Iman Katouzian wrote: > Hello, > > I have downloaded the toluene pdb file and want to use it as solvent in > GROMACS rather than the water molecules. I have added toluene as a molecule > using gmx solvate -cs toluene.gro however, in the next steps, it is not > added to the topol.top file and I cannot go-ahead to the next steps of > simulation. I'd be grateful if someone can help me with this issue as I > have not tried other solvents rather than water before. > > Thanks. > > On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian > wrote: > > > Hello, > > > > I have downloaded the toluene pdb file and want to use it as solvent in > > GROMACS rather than the water molecules. I have added toluene as a > molecule > > using gmx solvate -cs toluene.gro however, in the next steps, it is not > > added to the topol.top file and I cannot go-ahead to the next steps of > > simulation. I'd be grateful if someone can help me with this issue as I > > have not tried other solvents rather than water before. > > > > Thanks. > > > > -- > > > > *Iman Katouzian* > > > > *Ph.D.** candidate of Food Process Engineering* > > > > *Faculty of Food Science and Technology* > > > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > > > > > -- > > *Iman Katouzian* > > *Ph.D.** candidate of Food Process Engineering* > > *Faculty of Food Science and Technology* > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvent evaporation modeling
Den 2019-12-02 kl. 00:03, skrev SAKO MIRZAIE: Hi All, I want to simulate a polymer: protein system in a way that water solvent will evaporated gradually. How should I do that? What parameters are needed to be included in the mdp file. Best Alexandra Patriksson, Erik Marklund and David van der Spoel: Proteins Structures under Electrospray Conditions Biochemistry 46 pp. 933-945 (2007) Yaofeng Wang, Daniel Larsson and David van der Spoel: Encapsulation of Myoglobin in a CTAB micelle - A Simulation Study Biochemistry 48 pp. 1006-1015 (2009) Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel & Carl Caleman: Structural stability of electrosprayed proteins: temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) Friemann, Rosmarie; Larsson, Daniel; Wang, Yaofeng; Van der Spoel, David: Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in vacuo J. Amer. Chem. Soc. 131 pp. 16606-16607 (2009) And a review in David van der Spoel, Erik G. Marklund, Daniel S. D. Larsson and Carl Caleman: Proteins, Lipids and Water in the Gas Phase Macromolecular Bioscience 11 pp. 50-59 (2011) -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvent evaporation modeling
Dear André, Thank you very much for your email and hope Kalil has the script. Best regards On Mon, Dec 2, 2019 at 7:15 AM André Farias de Moura wrote: > Dear Sako, > > I'm ccing Kalil, who actually wrote and run the script to remove solvent > molecules, he might still have it. > > regards > > Andre > > On Mon, Dec 2, 2019 at 2:54 AM SAKO MIRZAIE > wrote: > >> Dear André, >> >> Thank you for your response. >> Could you send me such a script? >> >> On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura >> wrote: >> >>> Dear Sako, >>> >>> we did something like that a few years ago, please take a look at DOI >>> 10.1039/C4CP03519D >>> for details. >>> >>> in a nutshell: you need a script that runs a sequence of short >>> equilibration and production runs after a number of solvent molecules are >>> removed (implying that topology needs to be updated for the number of >>> solvent molecules at each round, so the script needs to include some >>> parsing of the files as well). >>> >>> Andre >>> >>> On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE >>> wrote: >>> Hi All, I want to simulate a polymer: protein system in a way that water solvent will evaporated gradually. How should I do that? What parameters are needed to be included in the mdp file. Best -- *** Sako -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >>> >>> >>> -- >>> _ >>> >>> Prof. Dr. André Farias de Moura >>> Department of Chemistry >>> Federal University of São Carlos >>> São Carlos - Brazil >>> phone: +55-16-3351-8090 >>> >> >> >> -- >> *** >> Sako Mirzaie >> Sako Mirzaie >> Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad >> University of Sanandaj, Sanandaj, Iran >> >> Visiting Professor, Advanced Pharmaceutics >> >> & Drug Delivery Laboratory >> >> Leslie Dan Faculty of Pharmacy >> >> University of Toronto >> >> 144 College Street, Toronto, Ontario >> >> Canada M5S 3M2 >> >> http://scholar.google.com/citations?user=viwZvVAJ=en >> >> http://www.scopus.com/authid/detail.url?authorId=54886431500 >> >> http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie >> https://www.researchgate.net/profile/Sako_Mirzaie/publications/ >> >> >> >> >> >> >> > > -- > _ > > Prof. Dr. André Farias de Moura > Department of Chemistry > Federal University of São Carlos > São Carlos - Brazil > phone: +55-16-3351-8090 > -- *** Sako Mirzaie -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to obtain the number of residue per turn with GROMACS ?
Hello, I would like to obtain the time serie of the number of residues per turn with GROMACS for a given peptide ? Is it possible to obtain this property with a GROMACS tool ? If yes, how ? Thank you Stéphane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] toluene as a slovent
Den 2019-12-02 kl. 17:10, skrev Mijiddorj B: I recommend you to use (1) gmx insert-molecules tool to fill the box that solvent molecule. For the number of molecules, you can use as much as a higher number using -nmol option. The result tells you, how many molecules inserted from ordered numbers. (2) Then, you should manually edit the topology file using the correct number of toluene. http://virtualchemistry.org/molecule.php?filename=toluene.sdf http://virtualchemistry.org/ff.php -- Message: 5 Date: Mon, 2 Dec 2019 12:14:21 +0330 From: Iman Katouzian To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] toluene as a slovent Message-ID: Content-Type: text/plain; charset="UTF-8" Hello, I have downloaded the toluene pdb file and want to use it as solvent in GROMACS rather than the water molecules. I have added toluene as a molecule using gmx solvate -cs toluene.gro however, in the next steps, it is not added to the topol.top file and I cannot go-ahead to the next steps of simulation. I'd be grateful if someone can help me with this issue as I have not tried other solvents rather than water before. Thanks. On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian wrote: Hello, I have downloaded the toluene pdb file and want to use it as solvent in GROMACS rather than the water molecules. I have added toluene as a molecule using gmx solvate -cs toluene.gro however, in the next steps, it is not added to the topol.top file and I cannot go-ahead to the next steps of simulation. I'd be grateful if someone can help me with this issue as I have not tried other solvents rather than water before. Thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 188, Issue 3 * -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] toluene as a slovent
I recommend you to use (1) gmx insert-molecules tool to fill the box that solvent molecule. For the number of molecules, you can use as much as a higher number using -nmol option. The result tells you, how many molecules inserted from ordered numbers. (2) Then, you should manually edit the topology file using the correct number of toluene. > > -- > > Message: 5 > Date: Mon, 2 Dec 2019 12:14:21 +0330 > From: Iman Katouzian > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] toluene as a slovent > Message-ID: > ffcoduoqogukzuuwcb_+tamo...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hello, > > I have downloaded the toluene pdb file and want to use it as solvent in > GROMACS rather than the water molecules. I have added toluene as a molecule > using gmx solvate -cs toluene.gro however, in the next steps, it is not > added to the topol.top file and I cannot go-ahead to the next steps of > simulation. I'd be grateful if someone can help me with this issue as I > have not tried other solvents rather than water before. > > Thanks. > > On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian > wrote: > > > Hello, > > > > I have downloaded the toluene pdb file and want to use it as solvent in > > GROMACS rather than the water molecules. I have added toluene as a > molecule > > using gmx solvate -cs toluene.gro however, in the next steps, it is not > > added to the topol.top file and I cannot go-ahead to the next steps of > > simulation. I'd be grateful if someone can help me with this issue as I > > have not tried other solvents rather than water before. > > > > Thanks. > > > > -- > > > > *Iman Katouzian* > > > > *Ph.D.** candidate of Food Process Engineering* > > > > *Faculty of Food Science and Technology* > > > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > > > > > -- > > *Iman Katouzian* > > *Ph.D.** candidate of Food Process Engineering* > > *Faculty of Food Science and Technology* > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > > > -- > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 188, Issue 3 > * > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimisation error
Dear All, Good morning. I am doing the Protein Ligand complex simulation tutorial from the Gromacs website. I followed the tutorial without any issue. When I want to run the energy minimisation md, i get the error message Fatal error: grid cell cx -2147483648 cy -2147483648 out of range (max 24 24) atom -nan -nan -nan, grid->c0 0.00 0.00 I suppose the system is blowing up. There is another error in the nohup file WARNING: Listed nonbonded interaction between particles 2615 and 2632 at distance 3.841 which is larger than the table limit 2.470 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Not sure which parameter to change How to resolve the error? I have Gromacs 2019.4 on an ASUS TUF laptop with AMD Ryzen processor. Thank you Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] npt.tpr protein-lig
Good day, I have generated npt.tpr for my protein ligand and changed my npt.mdp file according to the suggestions by GROMACS for using Brendsen and h-bonds for constraints finally I encounter this NOTE which I think will cause further problems in my md run : NOTE 1 [file topol.top, line 18260]: The bond in molecule-type UNL between atoms 6 C5 and 7 C6 has an estimated oscillational period of 1.8e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group Protein_UNL is 4960.82 Number of degrees of freedom in T-Coupling group Water_and_ions is 77850.18 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm I would appreciate it if someone tells me what I need to do with my system I think it may be related to the time step of my simulaiton and frames as I searched the similar issues. thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] toluene as a slovent
Hello, I have downloaded the toluene pdb file and want to use it as solvent in GROMACS rather than the water molecules. I have added toluene as a molecule using gmx solvate -cs toluene.gro however, in the next steps, it is not added to the topol.top file and I cannot go-ahead to the next steps of simulation. I'd be grateful if someone can help me with this issue as I have not tried other solvents rather than water before. Thanks. On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian wrote: > Hello, > > I have downloaded the toluene pdb file and want to use it as solvent in > GROMACS rather than the water molecules. I have added toluene as a molecule > using gmx solvate -cs toluene.gro however, in the next steps, it is not > added to the topol.top file and I cannot go-ahead to the next steps of > simulation. I'd be grateful if someone can help me with this issue as I > have not tried other solvents rather than water before. > > Thanks. > > -- > > *Iman Katouzian* > > *Ph.D.** candidate of Food Process Engineering* > > *Faculty of Food Science and Technology* > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
