Re: [gmx-users] Restart energy minimization with step .pdb files

(at least this is what I can see from ener.edr). Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: 27 February 2020 13:11 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Restart energy

Re: [gmx-users] Restart energy minimization with step .pdb files

On 2/27/20 4:37 AM, Michele Pellegrino wrote: Hi, I am trying to restart steepest descent using the .pdb files generated by mdrun. The name of these files has the following pattern: step#%_n*.pdb being # and * integers and % a character ('a', 'b' or 'c'). I read the documentation, but I

Re: [gmx-users] Restart energy minimization with step .pdb files

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Quyen V. Vu Sent: 27 February 2020 11:22 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Restart energy minimization with step .pdb files It usually happens when you have two or more atoms overlap

Re: [gmx-users] Restart energy minimization with step .pdb files

It usually happens when you have two or more atoms overlap. step_XXX.pdb is the lowest energy state that steepest descend can give you with your input file. In my opinion, you should look into the log file of energy minimization step, find out which atom is exerted the maximum force, visualize

[gmx-users] Restart energy minimization with step .pdb files

Hi, I am trying to restart steepest descent using the .pdb files generated by mdrun. The name of these files has the following pattern: step#%_n*.pdb being # and * integers and % a character ('a', 'b' or 'c'). I read the documentation, but I can't understand what those files represent.

Re: [gmx-users] Restart dynamics when trr files removed

On 5/14/19 10:34 AM, CROUZY Serge 119222 wrote: Hello Jon and Justin I had a MD simulation "dyn" running for 46 ns (actually it's 30 umbrella simulations using pull code) I did try the -cpi option and my calculation seems to have restarted correctly renaming the files dyn.part0003 But

Re: [gmx-users] Restart dynamics when trr files removed

95e-01, up2= 4.06699985e-01, fac= 1.e+00) functype[1044]=DISRES, label= 6, type=1, low= 3.0303e-01, up1= 3.0303e-01, up2= 4.3502e-01, fac= 1.e+00) etc... Any suggestions about what is wrong here would be appreciated Thanks, Eiso ---

Re: [gmx-users] Restart dynamics when trr files removed

On 5/13/19 8:20 AM, CROUZY Serge 119222 wrote: Dear Gromacs users I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp

Re: [gmx-users] Restart dynamics when trr files removed

Hi, > But NO - I can't restart the simulation from 50 ns on without trr files There should be a checkpoint file called (by default) state.cpt that was generated when your 50 ns simulation finished. You can use this file to continue your run from the final state of that simulation with: gmx

[gmx-users] Restart dynamics when trr files removed

Dear Gromacs users I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp and corrected mdp file (with nstxout=0)... But NO -

Re: [gmx-users] restart simulations

sys.kth.se On Behalf Of Mark Abraham Sent: 11 de janeiro de 2019 10:31 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] restart simulations Hi, If you want to append (because gmx mdrun -append is on by default), then mdrun will check that your output files are unchanged. Either leave them unchanged

Re: [gmx-users] restart simulations

Hi, If you want to append (because gmx mdrun -append is on by default), then mdrun will check that your output files are unchanged. Either leave them unchanged, or tell mdrun that you are not appending with gmx mdrun -noappend. Does the error message that I presume you saw suggest the latter?

[gmx-users] restart simulations

Dear all, although it is not necessary to restart the simulation, we need to have the trajectory file in the folder where the MD runs ?! Can we use a shorter trajectory file? Thank you! Rita Melo. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Restart

Hi, On Tue, Jul 31, 2018, 19:56 Eric Smoll wrote: > Hi Mark, > > Thanks for the reply. I do use directories for project management but, up > until now, I also had a preference for custom filenames. Lesson learned. > I need to use the default naming scheme if I want smooth restarts. You

Re: [gmx-users] Restart

Hi, You can find the file names that it looks for by doing gmx dump -cp state.cpt. On 31 July 2018 at 18:55, Eric Smoll wrote: > Hi Mark, > > Thanks for the reply. I do use directories for project management but, up > until now, I also had a preference for custom filenames. Lesson learned. >

Re: [gmx-users] Restart

Hi Mark, Thanks for the reply. I do use directories for project management but, up until now, I also had a preference for custom filenames. Lesson learned. I need to use the default naming scheme if I want smooth restarts. I wrongfully assumed that the consistent use of output filename flags

Re: [gmx-users] Restart

Hi, As you can probably see in the log file, mdrun is refusing to do the default restart with appending from the checkpoint because the output filenames when you wrote the files are different to the ones supplied by the mdrun defaults now. I'm sure the behavior of mdrun has been improved since

[gmx-users] Restart

Hello GROMACS users, I had a simulation terminate unexpectedly very close to completion and I would like to resume the simulation from a checkpoint file. my mdrun flags are -cpi, -s, -o, -x, -c, -e, -g, and -cpo. All of the associated files are present (except the -c file since there was a

Re: [gmx-users] restart nvt run

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you so so much for your reply Best regardsFarial Sent from Yahoo Mail for iPhone On Sunday, February 4,

Re: [gmx-users] restart nvt run

On 2/4/18 8:50 AM, farial tavakoli wrote: Dear Justin Thank you so much for replying  I dont know exactly how I should use gmx trjcat command to concatenate 2 .trr files (nvt.trr and traj.part0002.trr) I issued this command to merge them: gmx trjcat -f nvt.trr -o fixed.trr -cat but faced

Re: [gmx-users] restart nvt run

On 2/4/18 5:26 AM, farial tavakoli wrote: Dear GMX users I ran nvt simulation on my complex using gromacs2016.4. But faced to this error:File input/output error: Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space? so I deleted some files to make free space and

[gmx-users] restart nvt run

Dear GMX users I ran nvt simulation on my complex using gromacs2016.4. But faced to this error:File input/output error: Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space? so I deleted some files to make free space and then issued this command to restart the

Re: [gmx-users] Restart MD with overwritten CPT using TRR file in gromacs/2016.3

Hi, On Mon, Oct 30, 2017 at 6:55 PM Abramyan, Tigran wrote: > Thanks a lot for your response, Mark, > > > Your response did not come to my email, but I found it via Gromacs > website. I think my email is registered on your site, but I forgot my > Username. Is there a way

Re: [gmx-users] Restart MD with overwritten CPT using TRR file in gromacs/2016.3

Thanks a lot for your response, Mark, Your response did not come to my email, but I found it via Gromacs website. I think my email is registered on your site, but I forgot my Username. Is there a way to login with the email address and password? At the moment it looks like the only way I can

Re: [gmx-users] Restart MD with overwritten CPT using TRR file in gromacs/2016.3

Hi, There's always two cpt files on disk so this should never be needed, even if the parallel file system does the usual lie of telling mdrun that it has flushed to disk when it may or may not have done so... Mark On Fri, 27 Oct 2017 22:24 Abramyan, Tigran wrote: > Hi, >

[gmx-users] Restart MD with overwritten CPT using TRR file in gromacs/2016.3

Hi, Because one of my gromacs/2016.3 jobs accidentally crashed and got restarted and overwrote the CPT file, I am now attempting to continue a simulation using the TRR file. For this I ran the command 'gmx convert-tpr -s md.tpr -f md.trr -o md_next.tpr', so that I could use 'md_next.tpr' file

Re: [gmx-users] Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

Hi, Some of your commands and outputs are inconsistent. You can't get md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you don't use deffnm. But if you change that when trying to do your continuation, mdrun won't know how to append because you haven't told it that the old

[gmx-users] Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

Dear gmx users, I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a stopped simulation after a power failure? (used 8 processor cores + Graphics card GTX 780Ti). I have attached the log file along with this mail. It appeared that no details appended after restarting

Re: [gmx-users] Restart a stopped simulation after a power failure? correct command (Justin Lemkul) : gromacs.org_gmx-users Digest, Vol 156, Issue 81

vt.edu <mailto:jalem...@vt.edu>> To: gmx-us...@gromacs.org <mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] restart a stopped simulation after a power failure? correct command Message-ID: <c8f54875-63e8-3f17-50ea-c8fe506ec...@vt.edu <mai

Re: [gmx-users] restart a stopped simulation after a power failure? correct command (Justin Lemkul) : gromacs.org_gmx-users Digest, Vol 156, Issue 81

> > I also tried, mdrun -s md.tpr -cpi state.cpt -append > > Is it any modification required in command? > > Regards, > Adarsh V. K. > > > -- > > > > Message: 4 > > Date: Tue, 18 Apr 2017 08:21:56 -0400 > > From: Justin

Re: [gmx-users] restart a stopped simulation after a power failure? correct command (Justin Lemkul) : gromacs.org_gmx-users Digest, Vol 156, Issue 81

Message: 4 > Date: Tue, 18 Apr 2017 08:21:56 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] restart a stopped simulation after a power > failure? correct command > Message-ID: <c8f54875-63e8-3f17-50ea-c8

Re: [gmx-users] restart a stopped simulation after a power failure? correct command

On 4/18/17 1:21 AM, Adarsh V. K. wrote: Dear all, I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a stopped simulation after a power failure? I used the following command to restart the stopped simulation at 6.5 ns. *mdrun -s md.tpr -cpi state.cpt* Even Though the

[gmx-users] restart a stopped simulation after a power failure? correct command

Dear all, I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a stopped simulation after a power failure? I used the following command to restart the stopped simulation at 6.5 ns. *mdrun -s md.tpr -cpi state.cpt* Even Though the simulation appeared to be restarted successfully

Re: [gmx-users] Restart after crash

Hi, You'll have to look inside your log files to find out what mdrun decided it was able to do. Mark On Tue, Oct 4, 2016 at 5:21 AM Roshan Shrestha wrote: > I had restarted my crash run after around 271 ps. The simulation ran fine > after that and showed > > > > > > > > >

[gmx-users] Restart after crash

I had restarted my crash run after around 271 ps. The simulation ran fine after that and showed *starting mdrun 'Protein in water'250 steps, 5000.0 ps (continuing from step 135600,271.2 ps).step 2499900, remaining wall clock time: 1 s Writing final coordinates.step

Re: [gmx-users] Restart corrupted run

Hi, Nothing much has changed, e.g. follow http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Mark On Wed, Jul 13, 2016 at 12:02 PM Mehrnoosh Hazrati < mehrnoosh.hazr...@modares.ac.ir> wrote: > Hi all, > > how can I restart a MD run that stopped before finishing the calculations? > > I

Re: [gmx-users] Restart corrupted run

> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > It explains the restart procedure for version 4 and newer. > On 13 Jul 2016, at 12:01, Mehrnoosh Hazrati > wrote: > > Hi

[gmx-users] Restart corrupted run

Hi all, how can I restart a MD run that stopped before finishing the calculations? I know about the solution in previous versions of Gromacs, but now I'm working with Gromacs 5.1.2. Thank you in advance. Mehrnoosh -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] restart error

Great thank you! On 2016-06-23 09:39, Mark Abraham wrote: Hi, There's two possibilities here. 1) GROMACS has a bug with multi-simulation checkpointing - several people are reporting problems, and it's probably getting an overhaul for the 2016 release because it was far from clear the old

Re: [gmx-users] restart error

Hi, There's two possibilities here. 1) GROMACS has a bug with multi-simulation checkpointing - several people are reporting problems, and it's probably getting an overhaul for the 2016 release because it was far from clear the old version was always working 2) Your (parallel) file system isn't

[gmx-users] restart error

Dear Grommunity, When I try and restart with the command "mpiexec -np 192 mdrun_mpi -v -deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir simann59 simann60 simann61 simann62 simann63 simann64 simann65 simann66 simann67 simann68 simann69 simann70 simann71 simann72 simann73

Re: [gmx-users] Restart to continue a free energy calculations

On 6/20/16 9:40 AM, Alexander Alexander wrote: Dear gromacs user, My binding free energy calculation crashed while it was in the middle of the one of the lambda_state because of the time limit, I was wondering if it is possible to restart a crashed free energy calculation to continue around

[gmx-users] Restart to continue a free energy calculations

Dear gromacs user, My binding free energy calculation crashed while it was in the middle of the one of the lambda_state because of the time limit, I was wondering if it is possible to restart a crashed free energy calculation to continue around crashed pont without loosing accuracy and

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi all, After spending time for troubleshooting, I found that gromacs checkpoint/restart feature is working well. The failure occurred because I use root user to submit restart job (using slurm resource manager). After switching to non root user, the restart process is running. The reason why I

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

ok thanks > Hi, > > Yes, that's one way to work around the problem. In some places, a module > subsystem can be used to take care of the selection automatically, but you > don't want to set one up for just you to use. > > Mark > > On Sun, May 15, 2016 at 11:48 AM

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, Yes, that's one way to work around the problem. In some places, a module subsystem can be used to take care of the selection automatically, but you don't want to set one up for just you to use. Mark On Sun, May 15, 2016 at 11:48 AM wrote: > Thanks Mark, > > My

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Thanks Mark, My sysadmins have let me install my own GROMACS versions and have not informed me of any such mechanism. Would you suggest I qrsh into a node of each type and build an mdrun-only version on each? I'd then select a particular node type for a submit script with the relevant mdrun.

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, On Sat, May 14, 2016 at 1:09 PM wrote: > In case it's relevant/interesting to anyone, here are the details on our > cluster nodes: > > nodes # model # cores cpu model > RAM node_type > fmb01 - fmb33 33

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

In case it's relevant/interesting to anyone, here are the details on our cluster nodes: nodes # model # cores cpu model RAM node_type fmb01 - fmb33 33 IBM HS21XM 8 3 GHz Xeon E5450

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

On 5/14/16 3:48 AM, Husen R wrote: Hi, Currently I'm running this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html) to simulate restart with fewer nodes. at restart, I changed the amount of nodes from 3 to 2 nodes. I also changed the amount

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, Currently I'm running this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html) to simulate restart with fewer nodes. at restart, I changed the amount of nodes from 3 to 2 nodes. I also changed the amount of processes from 24 to 16 processes.

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

thanks a lot for your fast response. I have tried it, and it failed. I ask in this forum just to make sure. However, there was something in my cluster that probably make it failed. I'll handle it first and then retry to restart again. Regards, Husen On Sat, May 14, 2016 at 7:58 AM, Justin

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

On 5/13/16 8:53 PM, Husen R wrote: Dear all Does simulation able to be restarted from checkpoint file with fewer nodes ? let's say, at the first time, I run simulation with 3 nodes. At running time, one of those nodes is crashed and the simulation is terminated. I want to restart that

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager. On Sat, May 14, 2016 at 7:53 AM, Husen R wrote: > Dear all > > Does simulation able to be restarted from checkpoint file with fewer nodes > ? > let's say, at the first time, I run simulation with 3 nodes. At running

[gmx-users] Restart simulation from checkpoint file with fewer nodes

Dear all Does simulation able to be restarted from checkpoint file with fewer nodes ? let's say, at the first time, I run simulation with 3 nodes. At running time, one of those nodes is crashed and the simulation is terminated. I want to restart that simulation immadiately based on checkpoint

[gmx-users] Restart the interrupted program

hi allI performed 20 ns MD simulation, but in the middle of the simulation time, my run was interrupted twice and I restarted it. Now, despite the end of the simulation time and all the steps, the program not be interrupted? It is very important to me. Please help me. Thank you. -- Gromacs

Re: [gmx-users] restart issues with Gromacs

Hi, GROMACS assumes the file systems actually write to disk when you use the system call that means that, and works correctly if so. But if the file system or its configuration don't actually do that (for "performance" or erroneous reasons), then all bets are off. mdrun can't even know if it's

Re: [gmx-users] restart issues with Gromacs

Thanks Mark, Ok, so it sounds very much like it¹s on the cluster side. I¹ll fire this across to one of the sys admins and see if they can find out what the problem is, although I have no idea what and if they will find anything. >From the looks of it, the reading of the checkpoint file data was

Re: [gmx-users] Restart simulation after crash

Please don't reply to the entire digest, especially when you're not replying to anything related. On 9/26/15 1:44 PM, Juliano Braz Carregal wrote: Hi everyone,its possible to restart a MD simulation just after the power crashing instead restart from the beginning?thanks Of course.

[gmx-users] Restart simulation after crash

Hi everyone,its possible to restart a MD simulation just after the power crashing instead restart from the beginning?thanks Em 26/09/2015 7:00 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se escreveu: Send gromacs.org_gmx-users mailing list submissions to    

Re: [gmx-users] Restart -append

On 8/26/15 4:07 PM, Johnny Lu wrote: Dear Users, Simulation crashed. Gromacs 5.1 wrote last check point at about 4 min before the crash. Restart with mdrun -cpi (last check point file) -append Will the -append option get rid of the data for those 4 min between the last check point written

[gmx-users] Restart -append

Dear Users, Simulation crashed. Gromacs 5.1 wrote last check point at about 4 min before the crash. Restart with mdrun -cpi (last check point file) -append Will the -append option get rid of the data for those 4 min between the last check point written and the crash? Thank you. -- Gromacs

[gmx-users] Restart Arbitrary Frame Thermostat.

Hi. If I change ensemble (say, from NVT to NPT) but use the same thermostat/barostat, will the internal variables of the thermostat/barostat stays the same (like how many step later to couple the system to thermostat)? If I want to continue from a particular saved frame of the simulation (saved

Re: [gmx-users] Restart Arbitrary Frame Thermostat.

On Fri, Sep 19, 2014 at 6:39 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. If I change ensemble (say, from NVT to NPT) but use the same thermostat/barostat, will the internal variables of the thermostat/barostat stays the same (like how many step later to couple the system to thermostat)?

Re: [gmx-users] Restart Arbitrary Frame Thermostat.

Sorry for not being clear about the question. 1. If I start with NVT with thermostat A, and then continue with NPT with thermostat A, and barostat B, will the internal variables of thermostat A stays the same, upon transitioning from the NVT ensemble to NPT ensemble? 2. If I start with a NPT

Re: [gmx-users] Restart Arbitrary Frame Thermostat.

On Fri, Sep 19, 2014 at 7:23 PM, Johnny Lu johnny.lu...@gmail.com wrote: Sorry for not being clear about the question. 1. If I start with NVT with thermostat A, and then continue with NPT with thermostat A, and barostat B, will the internal variables of thermostat A stays the same, upon

Re: [gmx-users] Restart Arbitrary Frame Thermostat.

I ran gmxcheck on an old cpt file: Command line: gmxcheck -f nve1.cpt Checking file nve1.cpt Precision mismatch for state entry box, code precision is float, file precision is double Precision mismatch for state entry x, code precision is float, file precision is double Precision mismatch for

Re: [gmx-users] Restart Arbitrary Frame Thermostat.

I mean is the last frame ... time, the time for the frame of the cpt file, or the frame right before the frame of the cpt file? On Fri, Sep 19, 2014 at 3:28 PM, Johnny Lu johnny.lu...@gmail.com wrote: I ran gmxcheck on an old cpt file: Command line: gmxcheck -f nve1.cpt Checking file

Re: [gmx-users] Restart Arbitrary Frame Thermostat.

Just do it! ;-) mdrun -nsteps 1 Mark On Fri, Sep 19, 2014 at 9:29 PM, Johnny Lu johnny.lu...@gmail.com wrote: I mean is the last frame ... time, the time for the frame of the cpt file, or the frame right before the frame of the cpt file? On Fri, Sep 19, 2014 at 3:28 PM, Johnny Lu

[gmx-users] restart the calculation----- checksum error

Hello dear gmx-users, I tried to restart the calculation, but there is always one checksum error as: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c, line: 2155 Fatal error: Checksum wrong for 'pull.xvg'. The file has been replaced

Re: [gmx-users] restart the calculation----- checksum error

On 7/2/14, 5:59 AM, Guo, Yanan (IPC) wrote: Hello dear gmx-users, I tried to restart the calculation, but there is always one checksum error as: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c, line: 2155 Fatal error: Checksum

Re: [gmx-users] restart failed

On Sat, Nov 16, 2013 at 10:46 AM, xiao helitr...@126.com wrote: Hi all gromacs users, My simulation crashed, and i try to restart it by using the following command: mdrun -s topol.tpr -cpi state.cpt Not using -deffnm means mdrun expects to write traj.trr, traj.xtc, ener.edr... The