[gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation
Dear GROMACS users, I am new to GROMACS software and have a question about switching off pair-wise non-bonded interactions between two molecules. I have a simulation box composed of a protein with a substrate inside the protein catalytic pocket and there are no covalent bonds between protein amino acids and a substrate. I would like to run MD simulation of this system after switching off non-bonded interactions between one of the amino acids and a substrate (leaving all intra non-bonded interactions & inter non-bonded interactions between given amino acids and other amino acids). I would appreciate it a lot if you could guide me on how to do this. Below are approaches I tried but got warning/error messages: Approach 1) use [exlucsions] in .top file If, let's say, atom # 1,2,3 are for the amino acid and atom# 4,5 is for a substrate, I added: [ exclusions] 1 4 5 2 4 5 3 4 5 I have successfully obtained .tpr file from grompp but got a fatal error after mdrun: 'There is no domain decomposition for 448 ranks that is compatible with the given box and a minimum cell size of 25.3862 nm. Change the number of ranks or mdrun option -rdd or -dds' Approach 2) use energygrps and energygrp-excl in .mdp file If the name in the index for the amino acid and substrate is A and B respectively, I added: energygrps = A B energygrp-excl = A B Also, I knew that energygrp-excl does not support Verlet cut-off scheme, I used a 'group'. However, I have got an error message when I used grompp: 'The sum of the two largest charge group radii (33.381752) is larger than rlist (1.20)' Just to be clear below is a summary of my system: - a system composed of one protein and a small substrate - the substrate and amino acid that I would like to switch-off are charged (+1 and -1, respectively) - protein-substrate complex are solvated in TIP3P waters, total # of atoms in the system = ~450,000 First of all, I am not sure whether these approaches are correct to switch-off non-bonded interactions between two molecules. Second, if so, I would like to know how to correct these issues. Sincerely, Soomin -- 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] slurm, gres:gpu, only 1 GPU out of 4 is detected
I had the misconception that I have to set gpuid by CUDA_VISIBLE_DEVICES set by slurm. However, slurm exposes the gpu for gromacs by a different mechanism. On 11/13/19 4:55 PM, Tamas Hegedus wrote: Hi, I run gmx 2019 using GPU There are 4 GPUs in my GPU hosts. I have slurm and configured gres=gpu 1. If I submit a job with --gres=gpu:1 then GPU#0 is identified and used (-gpu_id $CUDA_VISIBLE_DEVICES). 2. If I submit a second job, it fails: the $CUDA_VISIBLE_DEVICES is 1 and selected, but GPU #0 is identified by gmx as a compatible gpu. From the output: gmx mdrun -v -pin on -deffnm equi_nvt -nt 8 -gpu_id 1 -nb gpu -pme gpu -npme 1 -ntmpi 4 GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC: no, stat: compatible Fatal error: You limited the set of compatible GPUs to a set that included ID #1, but that ID is not for a compatible GPU. List only compatible GPUs. 3. If I login to that node and run the mdrun command written into the output in the previous step then it selects the right gpu and runs as expected. $CUDA_DEVICE_ORDER is set to PCI_BUS_ID I can not decide if this is a slurm config error or something with gromacs, as $CUDA_VISIBLE_DEVICES is set correctly by slurm and I expect gromacs to detect all 4GPUs. Thanks for your help and suggestions, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta...@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.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] slurm, gres:gpu, only 1 GPU out of 4 is detected
Hi, I run gmx 2019 using GPU There are 4 GPUs in my GPU hosts. I have slurm and configured gres=gpu 1. If I submit a job with --gres=gpu:1 then GPU#0 is identified and used (-gpu_id $CUDA_VISIBLE_DEVICES). 2. If I submit a second job, it fails: the $CUDA_VISIBLE_DEVICES is 1 and selected, but GPU #0 is identified by gmx as a compatible gpu. From the output: gmx mdrun -v -pin on -deffnm equi_nvt -nt 8 -gpu_id 1 -nb gpu -pme gpu -npme 1 -ntmpi 4 GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC: no, stat: compatible Fatal error: You limited the set of compatible GPUs to a set that included ID #1, but that ID is not for a compatible GPU. List only compatible GPUs. 3. If I login to that node and run the mdrun command written into the output in the previous step then it selects the right gpu and runs as expected. $CUDA_DEVICE_ORDER is set to PCI_BUS_ID I can not decide if this is a slurm config error or something with gromacs, as $CUDA_VISIBLE_DEVICES is set correctly by slurm and I expect gromacs to detect all 4GPUs. Thanks for your help and suggestions, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta...@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.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] eelctric field
Dear Christian, Thank you for your reply. However, still it is not fully clear to me. Lets only talk about gmx energy. How it happens that I get from gmx energy similar values of energies (LJ, columbs, total energies) while a different pressure, with and without applied filed? The total energy should be different as a result of an additional energy due to applied filed on each atom. On Wed, Nov 13, 2019 at 3:10 PM Christian Blau wrote: > Hello Amin, > > > When you apply an electric field during the simulation by setting the mdp > parameters like E-x =... as you describe, > nothing more happens than that each atom experiences an additional force > that is "atom charge * field strength". The > energy terms or virial (that then would relate to pressure coupling) are > not influenced by this. If these terms differ > between a simulation with electric field and one without, then only > because the system as a whole responds to the > applied electric field. > > gmx potential on the other hand is an analysis tool that is per se > unrelated on how you chose to apply an electric field > during your simulation or not. However, when applying an electric field, > you would expect a different result from an > analysis with gmx potential than without electric field, because your > system will respond to the applied electric field. > > > Best, > > Christian > > On 11/13/19 2:44 PM, Amin Rouy wrote: > > Hi, > > > > I am using gromacs 5.0.4. I apply a uniform electric field in x direction > > of my box (no walls), > > E-x= 1 10 0, and simulation runs without error. > > I notice that the values of electrostatic interactions I get from the > > simulation is the same as without the an electric field. Which is > strange, > > but according to previous questions in the gromacs forum this is true: > > ''gmx potential only calculates the electric field and potential of the > > system. It does not take into account the applied field.'' > > > > Now, my question is are the other quantities obtaining from gmx energy > take > > into account field effect? e.g. pressure of the system. > -- > 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] eelctric field
Hello Amin, When you apply an electric field during the simulation by setting the mdp parameters like E-x =... as you describe, nothing more happens than that each atom experiences an additional force that is "atom charge * field strength". The energy terms or virial (that then would relate to pressure coupling) are not influenced by this. If these terms differ between a simulation with electric field and one without, then only because the system as a whole responds to the applied electric field. gmx potential on the other hand is an analysis tool that is per se unrelated on how you chose to apply an electric field during your simulation or not. However, when applying an electric field, you would expect a different result from an analysis with gmx potential than without electric field, because your system will respond to the applied electric field. Best, Christian On 11/13/19 2:44 PM, Amin Rouy wrote: Hi, I am using gromacs 5.0.4. I apply a uniform electric field in x direction of my box (no walls), E-x= 1 10 0, and simulation runs without error. I notice that the values of electrostatic interactions I get from the simulation is the same as without the an electric field. Which is strange, but according to previous questions in the gromacs forum this is true: ''gmx potential only calculates the electric field and potential of the system. It does not take into account the applied field.'' Now, my question is are the other quantities obtaining from gmx energy take into account field effect? e.g. pressure of the system. -- 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] eelctric field
sorry I use gromacs/2016.1. On Wed, Nov 13, 2019 at 2:44 PM Amin Rouy wrote: > Hi, > > I am using gromacs 5.0.4. I apply a uniform electric field in x direction > of my box (no walls), > E-x= 1 10 0, and simulation runs without error. > I notice that the values of electrostatic interactions I get from the > simulation is the same as without the an electric field. Which is strange, > but according to previous questions in the gromacs forum this is true: > ''gmx potential only calculates the electric field and potential of the > system. It does not take into account the applied field.'' > > Now, my question is are the other quantities obtaining from gmx energy > take into account field effect? e.g. pressure of the system. > -- 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] eelctric field
Hi, I am using gromacs 5.0.4. I apply a uniform electric field in x direction of my box (no walls), E-x= 1 10 0, and simulation runs without error. I notice that the values of electrostatic interactions I get from the simulation is the same as without the an electric field. Which is strange, but according to previous questions in the gromacs forum this is true: ''gmx potential only calculates the electric field and potential of the system. It does not take into account the applied field.'' Now, my question is are the other quantities obtaining from gmx energy take into account field effect? e.g. pressure of the system. -- 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] gmx rdf with surf option
Dear GMX users, I have a question regarding GMX RDF and I apologize if my question is too basic. My trajectory consists of a dimer inserted in a membrane with an explicit water/ion environment. I would like to compute the distribution of the center of mass of lipid molecules to the surface of the receptor. My first test consisted of the following command: 1) gmx rdf -f traj.xtc -s md.tpr -n index.ndx -o rdf_T1.xvg -surf mol -seltype whole_res_com I got the following error: Inconsistency in user input: -surf only works with -ref that consists of atoms When I run again the same command line but with -selrpos, it works "fine" 2) gmx rdf -f traj.xtc -s md.tpr -n index.ndx -o rdf_T1.xvg -surf mol -selrpos whole_res_com I know that COMs are not supported with -surf. But -seltype is supposed to be related to "the type of selection for the atom or group, residue, etc, we want to calculate the rdf for" no?. I can't understand why I got this error when using -seltype with -surf option. Any comment on this? In another test I tried this: 3) gmx rdf -f traj.xtc -s md.tpr -n index.ndx -o rdf_g15.xvg -surf mol -ref 'protein' -sel ''whole_res_com of group 15'' this one works fine but the output is different from the previous command (2). Although for me I was expecting the same results?! If none of these commands is correct, can you please tell me which option I can use in order to compute the RDF as the distribution of COM of lipid molecules to the surface of the protein, please? Thanks a lot. -- 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] (no subject)
thanks Prof. Justin On Tue, Nov 12, 2019 at 8:48 PM Justin Lemkul wrote: > > Please use an appropriate subject line. > > On 11/12/19 5:29 AM, shakuntala dhurua wrote: > > hello, > > Here I want to generate arg.pdb to arg.gro by using amber99sb force > field . > > for test i have used 1 residue of arginine but i got Fatal error: > > There is a dangling bond at at least one of the terminal ends and the > force > > field does not provide terminal entries or files. Fix your terminal > > residues so that they match the residue database (.rtp) entries, or > provide > > terminal database entries (.tdb). and following is the attach pdb format > > which i have used for pdb2gmx ,please suggest me to solve this problem > > AMBER does not support zwitterionic forms of single amino acids, at > least not within GROMACS. There may be a way to create such residues > from the AMBER parameter database, but you'll have to look into > published works on their force field parametrization to see if such > residue definitions exist. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] (no subject)
thanks Bratin for your suggestion On Tue, 12 Nov 2019, 7:54 pm Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: > I think you have capped your residue in the N-terminal and C-terminal > end...and the capping is not defined in your .rtp entry.. that's why this > error is coming > > On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, > wrote: > > > hello, > > Here I want to generate arg.pdb to arg.gro by using amber99sb force > field . > > for test i have used 1 residue of arginine but i got Fatal error: > > There is a dangling bond at at least one of the terminal ends and the > force > > field does not provide terminal entries or files. Fix your terminal > > residues so that they match the residue database (.rtp) entries, or > provide > > terminal database entries (.tdb). and following is the attach pdb format > > which i have used for pdb2gmx ,please suggest me to solve this problem > > -- > > 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. > -- 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] How to produce "gro" format for calcite {1014} structure.
Hi,
Maybe you could try to convert the cif format to pdb format, if you feel
that your conversion from cif to gro format is not working.
Best regards
Alessandra
On Tue, Nov 12, 2019 at 5:09 PM Hamid Zaree wrote:
> Hi.
> I would like to simulate Calcite structure in GROMACS. How could I make the
> structure of Calcite {1014}. And how could I make its topology.
> I was found a cif file in AMCSD data bank and a python script which
> produced a favourable shape of Calcite "gro" file; but:
>
> 1- The downloaded "Cif" file is not 1014 symmetry structure.
> 2- The final "gro" file (after implementing that python) has not molecule
> type and unfortunately, all Oxygen atoms as well the "Ca" and "C" came
> along each other and each Oxygen atom considered as a molecule in this
> "gro" file. In this case, I wasn't able to make a proper topology file. by
> any means.
> Special thanks!
> Shahryar.
> ---
> --
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