Re: [gmx-users] mdrun

Dear Dr Justin, Much appreciation. You nailed it. Kind regards. On Tue, Nov 5, 2013 at 2:41 PM, Justin Lemkul wrote: > > > On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote: > >> Dear Users, >> I am running MD simulations of a protein-ligand system. Sometimes when i >> do >> an mdrun, be it for the ene

Re: [gmx-users] mdrun

On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote: Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd

[gmx-users] mdrun

Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd way (strange extensions) e.g em.gro.tprr or md.

Re: [gmx-users] mdrun cpt

On Oct 29, 2013 1:26 AM, "Pavan Ghatty" wrote: > > Now /afterok/ might not work since technically the job is killed due to > walltime limits - making it not ok. Hence use -maxh! Mark > So I suppose /afterany/ is a better > option. But I do appreciate your warning about spamming the queue and ye

Re: [gmx-users] mdrun cpt

Now /afterok/ might not work since technically the job is killed due to walltime limits - making it not ok. So I suppose /afterany/ is a better option. But I do appreciate your warning about spamming the queue and yes I will re-read PBS docs. On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham wrote:

Re: [gmx-users] mdrun cpt

On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty wrote: > Mark, > > The problem with one .tpr file set for 100ns is that when job number (say) > 4 hits the wall limit, it crashes and never gets a chance to submit the > next job. So it's not really automated. > That's why I suggested -maxh, so you ca

Re: [gmx-users] mdrun cpt

You're welcome On 28 Oct 2013, at 20:03, Pavan Ghatty wrote: > Aah yes of course. Thanks James. > > > > On Mon, Oct 28, 2013 at 3:16 PM, wrote: > >> No this isn't a problem. You can use job names under the -hold_jid flag. >> As long as you change the job name in the submit script between >>

Re: [gmx-users] mdrun cpt

Aah yes of course. Thanks James. On Mon, Oct 28, 2013 at 3:16 PM, wrote: > No this isn't a problem. You can use job names under the -hold_jid flag. > As long as you change the job name in the submit script between > submissions this isn't a problem. You could have a submit script for job 4 > w

Re: [gmx-users] mdrun cpt

No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_

Re: [gmx-users] mdrun cpt

Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. But the PBS

Re: [gmx-users] mdrun cpt

On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty wrote: > I have need to collect 100ns but I can collect only ~1ns (1000steps) per > run. Since I dont have .trr files, I rely on .cpt files for restarts. For > example, > > grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 > > This run

Re: [gmx-users] mdrun cpt

I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits.

Re: [gmx-users] mdrun cpt

On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we can choose how often (time in mins) the .cpt file is written. B

[gmx-users] mdrun cpt

Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt

Re: [gmx-users] mdrun error

On 7/21/13 12:18 AM, Collins Nganou wrote: Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads --

[gmx-users] mdrun error

Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads --- P

Re: [gmx-users] mdrun no error, but hangs no results

Perhaps you need a less prehistoric compiler. Or the affinity-setting bug fix in 4.6.3. Or both. On Jul 17, 2013 6:25 PM, "Shi, Yu (shiy4)" wrote: > Dear gmx-users, > > My problem is weird. > My mdrun worked well using the old serial version 4.5.5 (about two years > ago). And I have these top, n

[gmx-users] mdrun no error, but hangs no results

Dear gmx-users, My problem is weird. My mdrun worked well using the old serial version 4.5.5 (about two years ago). And I have these top, ndx, mdp, and gro files. Basing on those old files, for the serial 4.6.2, the grompp works through, resulting the .tpr file successfully. After that when I m

Re: [gmx-users] mdrun segmentation fault for new build of gromacs 4.6.1

Hi, I recommend to run the regressiontests. The simplest way is to build GROMACS with cmake -DREGRESSIONTEST_DOWNLOAD, and run make check. See http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.12._Testing_GROMACS_for_correctness for more details. Roland On Thu, Jun 6, 2013

[gmx-users] mdrun segmentation fault for new build of gromacs 4.6.1

Gromacs users: I have just built and installed gromacs-4.6.1 on my Xeon 5500 compute cluster running Centos 5. The installation was done with gcc 4.7.0 I have run a simple test (the old tutor/gmxdemo) which fails at the first mdrun step with a segmentation fault. The command line for this ste

Re: [gmx-users] mdrun outputs incorrect resnames

Great, thank you that did the trick. My fault for not realizing this earlier. Best, Reid On Sun, May 26, 2013 at 2:12 AM, Tsjerk Wassenaar wrote: > No, the residue names are the those from the .top file. But that's not the > same as the moleculetypes. You have to change the residue names in th

Re: [gmx-users] mdrun outputs incorrect resnames

No, the residue names are the those from the .top file. But that's not the same as the moleculetypes. You have to change the residue names in the [ atoms ] section. Cheers, Tsjerk On Sun, May 26, 2013 at 12:57 AM, Mark Abraham wrote: > AFAIK, the residue names in the mdrun output .gro file are

Re: [gmx-users] mdrun outputs incorrect resnames

AFAIK, the residue names in the mdrun output .gro file are those of the structure file you gave to grompp. Mark On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn wrote: > Hello, > > I am simulating a lipid bilayer and wish to apply position restraints to > only a subset of the lipids in the bila

[gmx-users] mdrun outputs incorrect resnames

Hello, I am simulating a lipid bilayer and wish to apply position restraints to only a subset of the lipids in the bilayer. Since position restraints are applied to all molecules of the same molecule type, I defined a new molecule type (DOPR) which is identical to my lipid species (DOPC) by copyin

Re: [gmx-users] mdrun generate a lot of files with #

Or take your backup life into your own hands and set the environment variable GMX_MAXBACKUP=-1 Mark On Thu, May 23, 2013 at 7:04 PM, Justin Lemkul wrote: > > > On 5/23/13 12:53 PM, mu xiaojia wrote: > >> Dear users, >> >> I have used gromacs a while, however, sometime, when I run it on >> supe

Re: [gmx-users] mdrun generate a lot of files with #

On 5/23/13 12:53 PM, mu xiaojia wrote: Dear users, I have used gromacs a while, however, sometime, when I run it on supercomputer-clusters, I saw mdrun will generate a lot of files with "#", which occupied a lot of space, does anyone know why and how to avoid it? Thanks example, my command"m

[gmx-users] mdrun generate a lot of files with #

Dear users, I have used gromacs a while, however, sometime, when I run it on supercomputer-clusters, I saw mdrun will generate a lot of files with "#", which occupied a lot of space, does anyone know why and how to avoid it? Thanks example, my command"mdrun_mpi -s -deffnm job -cpi -append" then

Re: [gmx-users] mdrun and simulation time

thank you for the reply, I'm in contact with my admin and I hope that he will tell me something soon. One thing that I really don't understand is why only the last nanoseconds are "affected". I run the same simulation (with the same paramenters) and I've never had problems in the first 4 ns , only

Re: [gmx-users] mdrun and simulation time

On 5/13/13 6:41 AM, Francesco wrote: Good morning all, This morning I checked the output of a 8ns (4 x 2ns) of simulation and I noticed a strange behaviour: The fist two simulations (each 2ns) ended up correctly and they both took 2h 06min to finish. The second two were still running when the c

[gmx-users] mdrun and simulation time

Good morning all, This morning I checked the output of a 8ns (4 x 2ns) of simulation and I noticed a strange behaviour: The fist two simulations (each 2ns) ended up correctly and they both took 2h 06min to finish. The second two were still running when the cluster time was over (I asked for 2.30)

Re: [gmx-users] mdrun-gpu error message on Gromacs 4.5.5

On 5/6/13 9:39 PM, Andrew DeYoung wrote: Hi, I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM). This is my first time using a GPU. I get the following error message when attempting to run mdrun-gpu with my .tpr file: --- Program mdrun-

[gmx-users] mdrun-gpu error message on Gromacs 4.5.5

Hi, I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM). This is my first time using a GPU. I get the following error message when attempting to run mdrun-gpu with my .tpr file: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /usr/lo

Re: [gmx-users] mdrun on GPU

On 4/26/13 10:50 AM, Juliette N. wrote: Hi all, I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4. Can I use the same command line as before for mdrun or other tools? Please read through the docum

[gmx-users] mdrun on GPU

Hi all, I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4. Can I use the same command line as before for mdrun or other tools? Thank you very much, -- J. -- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] mdrun -rdd and -dds flag

On 11/04/2013 11:17, "manara r. (rm16g09)" wrote: >Dear gmx-users, > >I am having a problem with a periodic molecule and the domain >decomposition, I wish to use a high number of processors (circa 180, but >can obviously be reduced) and therefore need to use the -rdd or -dds >flags (I believe),

Re: [gmx-users] mdrun -rdd and -dds flag

On Thu, Apr 11, 2013 at 6:17 AM, manara r. (rm16g09) wrote: > Dear gmx-users, > > I am having a problem with a periodic molecule and the domain > decomposition, I wish to use a high number of processors (circa 180, but > can obviously be reduced) and therefore need to use the -rdd or -dds flags >

[gmx-users] mdrun -rdd and -dds flag

Dear gmx-users, I am having a problem with a periodic molecule and the domain decomposition, I wish to use a high number of processors (circa 180, but can obviously be reduced) and therefore need to use the -rdd or -dds flags (I believe), how do these value effect the simulation? The box size

Re: [gmx-users] mdrun WARING and crash

On 3/12/13 5:14 AM, l@utwente.nl wrote: Hallo Justin, Thank you for your reply, I uploaded the images, Please find following the link below, start box: http://s1279.beta.photobucket.com/user/Li_Liu/media/image0_zpsf95d10fe.jpeg.html?filters[user]=134822327&filters[recent]=1&filters[publi

RE: [gmx-users] mdrun WARING and crash

Lemkul [jalem...@vt.edu] Sent: Monday, March 11, 2013 10:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On Monday, March 11, 2013, wrote: > Hallo Justin, > > Thank you for your comments. > Taking your suggestions, I set nrexcl=1, and commen

RE: [gmx-users] mdrun WARING and crash

x-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Monday, March 11, 2013 10:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On Monday, March 11, 2013, wrote: > Hallo Justin, > > T

Re: [gmx-users] mdrun WARING and crash

Justin Lemkul [ > jalem...@vt.edu ] > Sent: Thursday, February 28, 2013 3:02 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] mdrun WARING and crash > > On 2/28/13 6:59 AM, l@utwente.nl wrote: > > Hallo Justin, > > > > Thank you for you help.

RE: [gmx-users] mdrun WARING and crash

for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On 2/28/13 6:59 AM, l@utwente.nl wrote: > Hallo Justin, > > Thank you for you help. I have read the previous discussions on this topic, > which is very helpful. > The link is: > http://gromacs.5086.n6.nabb

Re: [gmx-users] mdrun WARING and crash

On 2/28/13 6:59 AM, l@utwente.nl wrote: Hallo Justin, Thank you for you help. I have read the previous discussions on this topic, which is very helpful. The link is: http://gromacs.5086.n6.nabble.com/What-is-the-purpose-of-the-pairs-section-td5003598.html Well, there are still something

RE: [gmx-users] mdrun WARING and crash

cs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, February 27, 2013 4:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On 2/27/13 9:43 AM, l@utwente.nl wrote: > Dear Justin, > > Thank you for your reply. I have some other

Re: [gmx-users] mdrun WARING and crash

On 2/27/13 9:43 AM, l@utwente.nl wrote: Dear Justin, Thank you for your reply. I have some other questions, 1) Is it allowed to set nrexcl=0 in topology file in order to make every coarse-grained particles interact with each. Are there bonded interactions? If so, such an exclusion se

RE: [gmx-users] mdrun WARING and crash

[jalem...@vt.edu] Sent: Tuesday, February 26, 2013 6:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On 2/26/13 11:57 AM, l@utwente.nl wrote: > Dear all, > > I got WARNING after mdrun, which says: > > "WARNING: Listed nonbonded

Re: [gmx-users] mdrun WARING and crash

On 2/26/13 11:57 AM, l@utwente.nl wrote: Dear all, I got WARNING after mdrun, which says: "WARNING: Listed nonbonded interaction between particles 794 and 797 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction insid

[gmx-users] mdrun WARING and crash

Dear all, I got WARNING after mdrun, which says: "WARNING: Listed nonbonded interaction between particles 794 and 797 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a

Re: [gmx-users] mdrun error

On 8/9/12 1:40 PM, Shima Arasteh wrote: Dear gmx users, Would be this error (as you see here) a symptom of blowing up of a system? Or just .mdp options should be changed? Fatal error: 1 of the 16625 bonded interactions could not be calculated because some atoms involved moved further apart

[gmx-users] mdrun error

Dear gmx users, Would be this error (as you see here) a symptom of blowing up of a system? Or just .mdp options should be changed? Fatal error: 1 of the 16625 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.8176

Re: [gmx-users] mdrun-gpu

On 9/08/2012 3:47 PM, cuong nguyen wrote: Dear Gromacs Users, I am trying Gromacs/4.5.5-OpenMM on GPU with CUDA support. when I run grompp-gpu to generate the .tpr file, it worked well: grompp-gpu -f input_min.mdp -o min.tpr -c box1.g96 however, then I run mdrun-gpu "mdrun-gpu -s min -o min -c m

[gmx-users] mdrun-gpu

Dear Gromacs Users, I am trying Gromacs/4.5.5-OpenMM on GPU with CUDA support. when I run grompp-gpu to generate the .tpr file, it worked well: grompp-gpu -f input_min.mdp -o min.tpr -c box1.g96 however, then I run mdrun-gpu "mdrun-gpu -s min -o min -c min.g96 -x min -e min -g min", it was stopped

[gmx-users] mdrun -j still functional?

Has anyone been recently using the coupling feature of mdrun for parameterising? I used it many versions ago and have just been trying to use it today with 4.5.5, however I can't get it to work as it did previously. Currently you can't couple more than one set of charges (seems a bit weird th

Re: [gmx-users] mdrun graceful exit

On Fri, Jul 6, 2012 at 1:13 AM, Mark Abraham wrote: > > Possibly not. This might be another instance of the GROMACS team having not > put much effort into the EM code on the theory that it doesn't run for long > enough, so have enough time for developer effort to pay off in significantly > better

Re: [gmx-users] mdrun graceful exit

On 6/07/2012 2:46 AM, Elton Carvalho wrote: Dear gmx-people. I know that if you send a KILL signal do a mdrun instance running integrator = md it sets nsteps to the next NS step and exits gracefully, but I don't see it happening to minimization runs. Is it possible to send a signal ta minimizat

[gmx-users] mdrun graceful exit

Dear gmx-people. I know that if you send a KILL signal do a mdrun instance running integrator = md it sets nsteps to the next NS step and exits gracefully, but I don't see it happening to minimization runs. Is it possible to send a signal ta minimization instance of mdrun to make it exit as if ns

Re: [gmx-users] mdrun no structural output

On 7/3/12 5:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I wanted to do a minimization with mdrun but the only output I get is: 3m71_minim.edr 3m71_minim.log 3m71_minim.trr But no structure file like .pdb i.e. There was no error in the step before where I prepared t

[gmx-users] mdrun no structural output

Hi everybody, I wanted to do a minimization with mdrun but the only output I get is: 3m71_minim.edr 3m71_minim.log 3m71_minim.trr But no structure file like .pdb i.e. There was no error in the step before where I prepared the input file with grompp. My .mdp file looks like this: define

Re: [gmx-users] mdrun -v output

Thanks Peter for the clarification. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Jun 19, 2012 at 2:27 AM, Peter C. Lai wrote: > It actually depends on your shell/environment :-P > > On sun grid engine and derivatives, the you can have the scheduler capture > the stdout and stder

Re: [gmx-users] mdrun -v output

It actually depends on your shell/environment :-P On sun grid engine and derivatives, the you can have the scheduler capture the stdout and stderr output through the -o and -e parameters, respectively. On 2012-06-18 05:28:11PM +0530, Chandan Choudhury wrote: > On Mon, Jun 18, 2012 at 12:43 PM, Ja

Re: [gmx-users] mdrun -v output

On Mon, Jun 18, 2012 at 12:43 PM, Javier Cerezo wrote: > Information messages, such as those shown on the screen during mdrun are > output to stderr. So if you want to get them you should redirect as follows: > > mdrun -v -s md.tpr 2> verbose.txt > > In the case where you may need to get all out

Re: [gmx-users] mdrun -v output

Information messages, such as those shown on the screen during mdrun are output to stderr. So if you want to get them you should redirect as follows: mdrun -v -s md.tpr 2> verbose.txt In the case where you may need to get all output (from both stdout and stderr) you should use: mdrun -v -s m

[gmx-users] mdrun -v output

Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr > verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing l

Re: [gmx-users] mdrun -rerun

Thanks Mark. I have several polymer chains (single polymer type) each having 362 atoms. So in order to exclude all nonbonded interactions of a chain with itself I need to add about 362 lines in the top file. [exclusions] 1 2 3 362 2 3 4 362 3 4 5 ...362 . 358 .. 362 . . 360 361 362 (this i

Re: [gmx-users] mdrun -rerun

On 13/04/2012 10:44 AM, Juliette N. wrote: Hello all, I am trying to exclude a nonbonded interactions on the polymer chains using grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr and mdrun -rerun command. but when I issue the command above grompp takes many hours to finish and at t

Re: [gmx-users] mdrun -rerun

Hello all, I am trying to exclude a nonbonded interactions on the polymer chains using grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr and mdrun -rerun command. but when I issue the command above grompp takes many hours to finish and at the end grompp crashes (Killed). This even lea

Re: [gmx-users] mdrun segmentation fault

On 12/04/2012 3:30 PM, priya thiyagarajan wrote: hello sir, Thanks for your kind reply.. i am performing final md run for 60molecules .. after i submitted my job for 5ns, when i analyse the result my run is completed only for 314ps initially.. At this point, you should have looked at your .

Re: [gmx-users] mdrun -rerun

Juliette N. wrote: On 1 April 2012 20:17, Mark Abraham wrote: On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonbonded energies using mdrun rerun option. mdrun -rerun should break the total nonbo

Re: [gmx-users] mdrun -rerun

On 1 April 2012 20:17, Mark Abraham wrote: > On 2/04/2012 10:10 AM, Juliette N. wrote: >> >> Hi all, >> >> I have an enquiry regarding calculation of heat of vaporization by >> estimating intermolecular nonbonded energies using mdrun rerun option. mdrun >> -rerun should break the total nonbonded e

Re: [gmx-users] mdrun -rerun in parallel?

neighbour searching every configuration. Mark Best, -- Forwarded message -- From: Juliette N. Date: 1 April 2012 22:10 Subject: Re: [gmx-users] mdrun -rerun To: Discussion list for GROMACS users On 1 April 2012 22:07, Mark Abraham wrote: On 2/04/2012 12:05 PM, Juliett

[gmx-users] mdrun -rerun in parallel?

Hi all, Is there anyway mdrun -rerun can be used on multiple nodes? e.g. -nt? Best, -- Forwarded message -- From: Juliette N. Date: 1 April 2012 22:10 Subject: Re: [gmx-users] mdrun -rerun To: Discussion list for GROMACS users On 1 April 2012 22:07, Mark Abraham wrote

Re: [gmx-users] mdrun -rerun

On 1 April 2012 22:07, Mark Abraham wrote: > On 2/04/2012 12:05 PM, Juliette N. wrote: >> >> Thanks. One last question. So whats the new trr file provided by -o >> flag of mdrun rerun below? >> >> mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new > > > If it even writes one,

Re: [gmx-users] mdrun -rerun

On 2/04/2012 12:05 PM, Juliette N. wrote: Thanks. One last question. So whats the new trr file provided by -o flag of mdrun rerun below? mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new If it even writes one, it will be identical to the -rerun file. There's no way for t

Re: [gmx-users] mdrun -rerun

Thanks. One last question. So whats the new trr file provided by -o flag of mdrun rerun below? mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new >> On 1 April 2012 20:17, Mark Abraham  wrote: >>> >>> On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I ha

Re: [gmx-users] mdrun -rerun

On 2/04/2012 11:16 AM, Juliette N. wrote: On 1 April 2012 20:17, Mark Abraham wrote: On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonbonded energies using mdrun rerun option. mdrun -rerun should

Re: [gmx-users] mdrun -rerun

On 1 April 2012 20:17, Mark Abraham wrote: > On 2/04/2012 10:10 AM, Juliette N. wrote: >> >> Hi all, >> >> I have an enquiry regarding calculation of heat of vaporization by >> estimating intermolecular nonbonded energies using mdrun rerun option. mdrun >> -rerun should break the total nonbonded e

Re: [gmx-users] mdrun -rerun

On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonbonded energies using mdrun rerun option. mdrun -rerun should break the total nonbonded energy coming from nonboded energy of (different molecules

[gmx-users] mdrun -rerun

Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonbonded energies using mdrun rerun option. mdrun -rerun should break the total nonbonded energy coming from nonboded energy of (different molecules + a molecule with itself). By setting appropria

Re: [gmx-users] mdrun - topol.tpr

On 8/03/2012 6:09 PM, Siew Wen Leong wrote: mdrun looks for topol.tpr by default. specify "-s em.tpr" in your command Please look up what -deffnm is for. :-) Mark On Wed, Mar 7, 2012 at 8:33 PM, Lara Bunte > wrote: Hi After I used grompp -f em.md

Re: [gmx-users] mdrun - topol.tpr

mdrun looks for topol.tpr by default. specify "-s em.tpr" in your command On Wed, Mar 7, 2012 at 8:33 PM, Lara Bunte wrote: > Hi > > After I used > > > grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > to collect my files into one em.tpr file (which is the meaning of gromp as > fas as

Re: [gmx-users] mdrun - topol.tpr

On Wed, 2012-03-07 at 12:33 +, Lara Bunte wrote: > Hi > > After I used > > > grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > to collect my files into one em.tpr file (which is the meaning of gromp as > fas as I understand it) > > Then I start mdrun for energy minimization wit

[gmx-users] mdrun - topol.tpr

Hi After I used grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr to collect my files into one em.tpr file (which is the meaning of gromp as fas as I understand it) Then I start mdrun for energy minimization with the command mdrun -nt 1 deffnm em and got the error Can not open file:

Re: [gmx-users] MDrun append...

general, but figured the former and was not such a big deal, so never wrote here. Stephan Original-Nachricht > Datum: Fri, 02 Mar 2012 17:31:49 +1100 > Von: Mark Abraham > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] MDrun append... > On 2/

Re: [gmx-users] MDrun append...

On 2/03/2012 3:59 PM, rama david wrote: Dear GROMACS Friends, my MD run get crashed , I foollow following command .. mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g protein_md.log -cpi -append -v the system respond in a way.. Fatal error: The original run wrote a file called

[gmx-users] MDrun append...

Dear GROMACS Friends, my MD run get crashed , I foollow following command .. mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g protein_md.log -cpi -append -v the system respond in a way.. Fatal error: The original run wrote a file called 'traj.trr' which is larger than 2 GB, but m

Re: [gmx-users] mdrun -multi flag

On 2/03/2012 10:15 AM, bo.shuang wrote: Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more

[gmx-users] mdrun -multi flag

Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more information and tips for troubleshooting, p

Re: [gmx-users] mdrun -pd

On Wed, Feb 29, 2012 at 1:47 PM, Mark Abraham wrote: > On 1/03/2012 12:31 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> I am trying to use option -p of mdrun for particle decomposition. >> I used: >> >> mpiexec mdrun -pd -deffnm nvt >> >> I obtain: >> >> apps/intel/ict/mpi/3.1.038/**bin/mpdli

Re: [gmx-users] mdrun -pd

On 1/03/2012 12:31 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to use option -p of mdrun for particle decomposition. I used: mpiexec mdrun -pd -deffnm nvt I obtain: apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead

Re: [gmx-users] mdrun extension and concatenation

On 28/02/2012 3:50 PM, priya thiyagarajan wrote: hello sir, while performing simulation for 30ns, because of queue time limit my run terminated at 11.6ns.. then i extended my simulation using mdrun as you suggest.. while doing so i got error as Fatal error: Failed to lock: md20.log. Functio

[gmx-users] mdrun extension and concatenation

hello sir, while performing simulation for 30ns, because of queue time limit my run terminated at 11.6ns.. then i extended my simulation using mdrun as you suggest.. while doing so i got error as Fatal error: Failed to lock: md20.log. Function not implemented. For more information and tips for t

Re: [gmx-users]mdrun using old version

On 26/02/2012 10:42 PM, nicolas prudhomme wrote: Hi gmx-users, I don't know why, but my mdrun suddenly started to use the 4.0.7 version while I have installed only the 4.5.4 version. I have reinstalled gromacs 4.5.4 but when I run mdrun it still want to use the 4.0.7 version and can not read

[gmx-users]mdrun using old version

Hi gmx-users, I don't know why, but my mdrun suddenly started to use the 4.0.7 version while I have installed only the 4.5.4 version. I have reinstalled gromacs 4.5.4 but when I run mdrun it still want to use the 4.0.7 version and can not read the tpr file. Thanks in advance for your help. N

Re: [gmx-users] mdrun on GROMACS 3.3.1

Hi, sorry I'm back to this thread after quite a long time, as I was trying to solve other problems. Now I'm back to the reverse transformation tutorial on the martini webpage and whenever I try to use the mdp script provided there for the annealing I just end up with the same error message, which i

Re: [gmx-users] mdrun on GROMACS 3.3.1

francesca vitalini wrote: Well I'm keeping struggling with this script. Apparently the problem in in using the integrator md with the GOMACS 3.3.1 version. In fact the same .mdp file with integrator steep works. while with md it always gives the error message that it cannot open the .xtc file

Re: [gmx-users] mdrun on GROMACS 3.3.1

Well I'm keeping struggling with this script. Apparently the problem in in using the integrator md with the GOMACS 3.3.1 version. In fact the same .mdp file with integrator steep works. while with md it always gives the error message that it cannot open the .xtc file. How can I get around this prob

Re: [gmx-users] mdrun on GROMACS 3.3.1

Thank you Justin for your quick reply. Unfortunately I cannot use a more modern version of GROMACS as my topology and .gro files where first created for a reverse transformation from cg to fg and thus required the 3.3.1 version and some specific .itp files that are only present in that version

Re: [gmx-users] mdrun on GROMACS 3.3.1

Francesca Vitalini wrote: Actually the directory is of my own and I have created it in my home directory so that shouldn't be a problem as I also have created other files in the same directory without any problems so far. Other ideas? Thanks Francesca Il giorno 31/gen/2012, alle ore 13.0

Re: [gmx-users] mdrun on GROMACS 3.3.1

Actually the directory is of my own and I have created it in my home directory so that shouldn't be a problem as I also have created other files in the same directory without any problems so far. Other ideas? Thanks Francesca Il giorno 31/gen/2012, alle ore 13.02, Justin A. Lemkul ha scritto:

Re: [gmx-users] mdrun on GROMACS 3.3.1

francesca vitalini wrote: Hallo GROMACS users! I'm trying to run a simple md script after running an energy minimization script on my system and I'm getting a wired error message Reading file dynamin_dimer_PR1.tpr, VERSION 3.3.1 (single precision) Loaded with Money -

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