[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Hi, I am using gromacs-2019.4. I have been running simulations box that contains a peptide embedded in a DOPC bilayer membrane, using all atom simulations. I have been running for weeks in a TACC computer that has 4 gpu in a single node, so I usually run 4 trajectories in a single node using the -multidir option. My submission script is: #!/bin/bash #SBATCH -J sb16 # Job name #SBATCH -o test.o%j # Job name #SBATCH -e test.e%j # Job name #SBATCH -N 1 # Total number of nodes requested #SBATCH -n 4# Total number of mpi tasks requested #SBATCH -p rtx # Queue (partition) name -- normal, development, etc. #SBATCH -t 48:00:00 # Run time (hh:mm:ss) - 1.5 hours module load cuda/10.1 module use -a /home1/01247/alfredo/Software/ForGPU/plumed-2.5.3/MyInstall/lib/plumed/ModuleFile module load plumed_gpu export OMP_NUM_THREADS=4 ibrun /home1/01247/alfredo/Software/gromacs-2019.4_gpu/build-gpu-mpi-plumed/My_install/bin/mdrun_mpi -s topol.tpr -plumed plumed.dat -multidir 1 2 3 4 Because the system is going to be down for a week I want to do continuation runs in a slower computer system, also using gpus. Because the system is slower I want to run it using two nodes. A script that I have used successfully in that old machine is: #!/bin/bash #SBATCH -J SB9_pi1 # Job name #SBATCH -o test.o%j # Job name #SBATCH -N 2 # Total number of nodes requested #SBATCH -n 2# Total number of mpi tasks requested #SBATCH -p gpu # Queue (partition) name -- normal, development, etc. #SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 1.5 hours module load gcc/5.2.0 module load cray_mpich/7.7.3 module load cuda/9.0 # Launc hMPI-based executable export OMP_NUM_THREADS=6 ibrun /home1/01247/alfredo/gromacs-2019.4/build_MPI/My_install/bin/mdrun_mpi -s topol2.tpr -pin on -cpi state.cpt -noappend It works great if I setup a new simulation of the same molecular system (create a new tpr file). But if I attempt to run a continuation run coming from the other machine (that used 4 threads). I get Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond of 10801 missing -5 U-B of 53187 missing 22 Proper Dih. of 89703 missing119 LJ-14 of 73729 missing 3 srun: Job step aborted: Waiting up to 32 seconds for job step to finish. And it stops. If I modified the script for the old machine to use 1 nodes, 1 task and 4 thread, it runs well but it is a lot slower. My question is if there is any way to avoid this error, so I can do a continuation run using state.cpt with a different domain decomposition. I have seen in the list that is suggested to use -rdd. The value printed in the log file is 1.595 nm. I increased to 2.0 and gave a similar error. Thanks, Alfredo -- 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] Script for looping n simulations
On 3/10/20 3:20 PM, Neena Susan Eappen wrote:
Hi Justin,
I tried that script out, but I want the output in a different way. So I have n
log files (.log), and I want to extract potential energy value say from line x
from all n log files. Is there a way I can export all these potential energy
values into one text file with one script?
Yes, this is easy to do with standard Linux tools, but that is a topic
for other forums. It is easier to get this information from .edr files
directly from gmx energy.
-Justin
Many thanks,
Neena
From: Neena Susan Eappen
Sent: Saturday, February 22, 2020 4:28 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Script for looping n simulations
Thank you Miro, but I don't think I found what I wanted in your script. Let me
be more clear: I ran n simulations in a loop, I have corresponding n energy
files (.edr). I want to extract potential energy from each file. How would I go
about that with a script?
Many thanks,
Neena
From: Neena Susan Eappen
Sent: Saturday, February 22, 2020 2:41 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Script for looping n simulations
Thank you Justin, just sharing the sample script here:
#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr
gmx mdrun -deffnm md${j}
done
--
Question: Now that I have n .edr files, is there a script I can write to
extract say potential energy from these n files?
Thank you for your time and knowledge,
Neena
From: Neena Susan Eappen
Sent: Saturday, February 15, 2020 4:44 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Script for looping n simulations
Hello gromacs users,
I was wondering how to write a script to repeat a simulation (equilibration and
production) n times, with each cycle starting with structure from the end of
previous cycle.
Many thanks,
Neena
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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Re: [gmx-users] Script for looping n simulations
Hi Justin,
I tried that script out, but I want the output in a different way. So I have n
log files (.log), and I want to extract potential energy value say from line x
from all n log files. Is there a way I can export all these potential energy
values into one text file with one script?
Many thanks,
Neena
From: Neena Susan Eappen
Sent: Saturday, February 22, 2020 4:28 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Script for looping n simulations
Thank you Miro, but I don't think I found what I wanted in your script. Let me
be more clear: I ran n simulations in a loop, I have corresponding n energy
files (.edr). I want to extract potential energy from each file. How would I go
about that with a script?
Many thanks,
Neena
From: Neena Susan Eappen
Sent: Saturday, February 22, 2020 2:41 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Script for looping n simulations
Thank you Justin, just sharing the sample script here:
#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr
gmx mdrun -deffnm md${j}
done
--
Question: Now that I have n .edr files, is there a script I can write to
extract say potential energy from these n files?
Thank you for your time and knowledge,
Neena
From: Neena Susan Eappen
Sent: Saturday, February 15, 2020 4:44 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Script for looping n simulations
Hello gromacs users,
I was wondering how to write a script to repeat a simulation (equilibration and
production) n times, with each cycle starting with structure from the end of
previous cycle.
Many thanks,
Neena
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gmx-developers] The setup of gpu_id has a bug?
Hi, Please sue the user's mailing list for questions not related to GROMACS development. By default. the "-gpu_id" option takes a sequence of digits corresponding to the numeric identifiers of GPUs. In cases where there are >10 GPUs in a system, a comma-separated string should be used, see http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node Cheers, -- Szilárd On Tue, Mar 10, 2020 at 5:51 PM dxli75 wrote: > everyone, >When I set the gpu_id as 10-15, the GMX always give the message of > PP:1,PME:1. > And the job run on GPU No.1 instead of No.10-15. >Is there a bug? > > GROMACS: gmx mdrun, version 2020.1 > > Executable: > /raid/data/dxli/projects/ncovs-1rpb/../../gromacs-2020.1/bin/gmx > Data prefix: /raid/data/dxli/projects/ncovs-1rpb/../../gromacs-2020.1 > Working dir: /raid/data/dxli/projects/ncovs-1rpb > Command line: > gmx mdrun -deffnm test -gpu_id 10 -ntmpi 1 -ntomp 8 > > Reading file test.tpr, VERSION 2020 (single precision) > 1 GPU selected for this run. > Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: > PP:1,PME:1 > PP tasks will do (non-perturbed) short-ranged interactions on the GPU > PP task will update and constrain coordinates on the CPUPME tasks will do > all aspects on the GPU > Using 1 MPI thread > > Non-default thread affinity set, disabling internal thread affinity > > Using 8 OpenMP threads > > > > > > > -- > *Daixi Li * > *Ph.D., Associated Professor**P.I.*, Laboratory of Computational Biology > > > > -- > Gromacs Developers mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-developers > or send a mail to gmx-developers-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] Replicate a structure
> Then my command would be gmx genconf -f system.gro -nbox 2 1 1 -o > new_system.gro right?? Based on what you described, I'd say that's correct. Try it out and then visualize the resulting .gro file to see if things are how you want them to be. > > On Tue, Mar 10, 2020, 6:01 PM John Whittaker < > johnwhitt...@zedat.fu-berlin.de> wrote: > >> Probably better to use gmx genconf; This situation is probably its main >> purpose. >> >> - John >> >> > Gmx editconf you can use with -translate flag...after that merz the >> > coordinates of two water droplets. I hope this may help you. >> > >> > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < >> > devargyachakraborty@gmail.com> wrote: >> > >> >> I have an equilibrated droplet of water. What I want to do is >> replicate >> >> that droplet in the x direction. So that my simulation box will carry >> >> two >> >> water droplets. Is that possible in gromacs. If yes please guide me. >> >> >> >> Thank you >> >> Devargya Chakraborty >> >> -- >> >> 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. >> > -- > 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] Replicate a structure
Then my command would be gmx genconf -f system.gro -nbox 2 1 1 -o new_system.gro right?? On Tue, Mar 10, 2020, 6:01 PM John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > Probably better to use gmx genconf; This situation is probably its main > purpose. > > - John > > > Gmx editconf you can use with -translate flag...after that merz the > > coordinates of two water droplets. I hope this may help you. > > > > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < > > devargyachakraborty@gmail.com> wrote: > > > >> I have an equilibrated droplet of water. What I want to do is replicate > >> that droplet in the x direction. So that my simulation box will carry > >> two > >> water droplets. Is that possible in gromacs. If yes please guide me. > >> > >> Thank you > >> Devargya Chakraborty > >> -- > >> 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. > -- 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] Replicate a structure
Probably better to use gmx genconf; This situation is probably its main purpose. - John > Gmx editconf you can use with -translate flag...after that merz the > coordinates of two water droplets. I hope this may help you. > > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < > devargyachakraborty@gmail.com> wrote: > >> I have an equilibrated droplet of water. What I want to do is replicate >> that droplet in the x direction. So that my simulation box will carry >> two >> water droplets. Is that possible in gromacs. If yes please guide me. >> >> Thank you >> Devargya Chakraborty >> -- >> 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] Clarification on the "-surface" and "-output" options of "gmx sasa"
On Mon, Mar 9, 2020 at 2:47 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > > > There seems to be very little explanation on the "-surface" and "-output" > options of "gmx sasa": > -surface: This should always consist of all non-solvent atoms in the > system. The area of this group is always calculated > -output: can specify additional selections, which should be subsets of the > calculation group. > > > Can I understand in this way: > > > 1. The "-surface" will calculate the surface area of the suppiled group. > Regardless the group is inside or outside of the protein, the "sasa" will > always assume the group to be fully solvent-exposed. So actually, it is not > "Solvent Accessible Surface Area" of the group; it is "taking the group out > from the protein, and put it in solvent, then calculate its surface". > > > 2. When all the residues are supplied to the "-output" option, I have > tested that the sum of "-output" equals to the "-surface": > gmx sasa -s protein.pdb -o area.xvg -tu ns -surface 'group 1' -output > 'resnr 1; resnr 2; resnr 3; ...; resnr n' > This is good. However, I saw many residues having area of 0 even though > they locate on the very outer surface. I think the explanation could be, > their side-chains are totally shielded by their neighbouring side-chains. > Is that correct? (I just feel SASA value of 0 is almost impossible) > > To calculate the surface a radii of 0.14 nm is used for the solvent probe, and also a radii is associated to each atom belonging the surface (for the values of the radii see the reference Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284). Thus it could be that atoms are shielded by other atoms volume or not accessible to the water bead. Best regards Alessandra > > Thank you! > > > Yours sincerely > Cheng > -- > 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] Setting a electric field in a simulation
Den 2020-03-10 kl. 03:17, skrev Mijiddorj B: Dear GMX users, I would like to perform MD simulations of solutions applying electric fields such as the microwave heating process. Is it possible to perform in gromacs? 1. How can I set the external electric field in the simulations? (from the user guide, I understood that I need to set 4 values electric-field-x = 2.0 150 5 0 How can I adjust the 2.45 GHz frequency? If you do not mind, please guide me. Best regards, Mijiddorj Why don't you try to play around and check the output file field.xvg to see what frequency you get? -- 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.
