[gmx-users] parallel running

Dear All I want to run gromacs in parallel on cluster.for this I follow below steps: 1-I connect to a node with ssh comand,fro example: ssh compute-o-1 2-cd scratch 3-grompp -f md.mdp-c input.gro-o output.tpr -p topol.top -n index.ndx 4- nohup mpirun -np 8 mdrun -de

Re: [gmx-users] parallel running

You don't use qsub or bsub? usually you should submit a script file containing the gromacs command, then bsub/qsub will allocate the required resource to your job. Jianguo From: mohsen ramezanpour To: Discussion list for GROMACS users Sent: Tuesday, 8 March

Re: [gmx-users] parallel running

On Mar 8, 2011, at 10:26 , mohsen ramezanpour wrote: > 4- nohup mpirun -np 8 mdrun -deffnm output & > > The result is running mdrun on one node(compute-0-1) (on its 4 CPUs) That's just as it is supposed to be. > Besides when I used the following command I get an executeable Error: >

[gmx-users] OPLS force field for RNA nucleotides for protein RNA simulation

Hello I am running a protein-RNA simulation, and was unable to find OLPS-AA topologies for RNA nucleotides. I am aware AMBER or CHARMM are the best force fields for nucleotides, but my protein only simulations were done in OPLS. Can I get any help with OPLS-AA topologies for, say, GMP compatible w

Re: [gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)

Thank you! I will try to change something and write to you about the result . -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

Re: [gmx-users] RMSD truncation Restart simulation problems

Hi All, hi Mark, Here are some more details. The outputs and error messages are attached at the end of the e-mail. After truncation I get the error message [1a], gromacs has problems with the checksum of the trr fles. After truncation the trajectories (xtc, trr) have the same length of 27752 frames

Re: [gmx-users] parallel running

On Tue, Mar 8, 2011 at 1:36 PM, Jianguo Li wrote: > You don't use qsub or bsub? > No,What is these?How can I prepare and use them? Thanks in advance > usually you should submit a script file containing the gromacs command, > then bsub/qsub will allocate the required resource to your job. > Jia

[gmx-users] g_energy inconsistent results

Dear Gromacs users, I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). The last stage is the following: grompp

Re: [gmx-users] parallel running

On Tue, Mar 8, 2011 at 1:40 PM, Esztermann, Ansgar < ansgar.eszterm...@mpi-bpc.mpg.de> wrote: > > On Mar 8, 2011, at 10:26 , mohsen ramezanpour wrote: > > > 4- nohup mpirun -np 8 mdrun -deffnm output & > > > > The result is running mdrun on one node(compute-0-1) (on its 4 CPUs) > > That'

Re: [gmx-users] parallel running

>> You don't use qsub or bsub? > > No,What is these?How can I prepare and use them? They are commands to submit jobs to batch systems. A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] parallel running

On Mar 8, 2011, at 12:00 , mohsen ramezanpour wrote: > >> > Besides when I used the following command I get an executeable Error: >> > mpirun -np 8 mdrun_mpi -deffnm output & >> >> What is the error message? > > the Error is: > Failed to find the following executable: > > Host:

Re: [gmx-users] Instantaneous Square Displacement

Mark Abraham wrote: On 8/03/2011 3:01 AM, Jennifer Williams wrote: Hi, I am writing a paper where I describe that gas molecules move inside a pore and then stick for long periods of time in occlusions in the pore wall. A reviewer has mentioned that I could illustrate this effect by using

Re: [gmx-users] QMMM

Good luck. I followed the instructions and was not successful. On Tue, Mar 8, 2011 at 12:48 AM, Haresh wrote: > Hello everyone, > > I want install gromacs with mopac7 for qmmm. > > Can you guide me for installation procedure > > Thank you. > > > -- > gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] g_energy inconsistent results

On 8/03/2011 9:44 PM, Ehud Schreiber wrote: Dear Gromacs users, I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). Th

Re: [gmx-users] RMSD truncation Restart simulation problems

On 8/03/2011 9:41 PM, Henri Mone wrote: Hi All, hi Mark, Here are some more details. The outputs and error messages are attached at the end of the e-mail. After truncation I get the error message [1a], gromacs has problems with the checksum of the trr fles. After truncation the trajectories (xtc,

Re: [gmx-users] parallel running

On Tue, Mar 8, 2011 at 2:53 PM, Esztermann, Ansgar < ansgar.eszterm...@mpi-bpc.mpg.de> wrote: > > On Mar 8, 2011, at 12:00 , mohsen ramezanpour wrote: > > > >> > Besides when I used the following command I get an executeable Error: > >> > mpirun -np 8 mdrun_mpi -deffnm output & > >> >

Re: [gmx-users] parallel running

On Tue, Mar 8, 2011 at 2:49 PM, Esztermann, Ansgar < ansgar.eszterm...@mpi-bpc.mpg.de> wrote: > > >> You don't use qsub or bsub? > > > > No,What is these?How can I prepare and use them? > > They are commands to submit jobs to batch systems. > > thank you.Please let me know more if it is possible T

Re: [gmx-users] parallel running

mohsen ramezanpour wrote: On Tue, Mar 8, 2011 at 2:49 PM, Esztermann, Ansgar > wrote: >> You don't use qsub or bsub? > > No,What is these?How can I prepare and use them? They are commands to submit jobs to batch systems. thank

Re: [gmx-users] parallel running

Dear Dr.Justin Thank you for your notice. I don't know the problem is related to MY COMMAND or to CLUSTER CONFIGURATION. please look at my commands and let me know the answer of this question.just this. Thanks in advance for your reply Mohsen On Tue, Mar 8, 2011 at 6:07 PM, Justin A. Lemkul wrote

Re: [gmx-users] parallel running

On 9/03/2011 1:51 AM, mohsen ramezanpour wrote: Dear Dr.Justin Thank you for your notice. I don't know the problem is related to MY COMMAND or to CLUSTER CONFIGURATION. please look at my commands and let me know the answer of this question.just this. The command you posted said that your comp

[gmx-users] Membrane Protein Tutorial

Dear All doing membrane protein tutorial of Dr.Justin I have a few question, Please let me know their answers. 1-Why do I need to use a tempreture upper than lipid phase transition tempreture for equilibration section? 2-What the lipid phase transition means exactly? Thanks in advance for you

[gmx-users] membrane-protein

Dear All doing membrane protein tutorial of Dr.Justin I have a few question, 1-Why do I need to know the stabilization state of my box vector? 2-How can I do this (with wich program?)? 3-What can I do if they were not stable? Thanks in advance Mohsen -- gmx-users mailing listgmx-users@gro

Re: [gmx-users] Tweeking MDP file options to run on GPU

Hi, What is the error you are getting? What is unfortunate about temperature coupling? Have you checked out the part of the documentation, especially the supported features on GPUs part (http://www.gromacs.org/gpu#Supported_features)? -- Szilárd On Mon, Mar 7, 2011 at 3:43 PM, kala wrote: >

RE: [gmx-users] Membrane Protein Tutorial

Below a certain temperature lipids form a gel or crystalline phase. If you run it at below that temperature, then it will behave nothing like a biological lipid membrane. (unless of course, that is what you want) Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Instit

[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault

New to Gromacs. Worked my way through the tutorial with relatively few issues until the Equilibration stage. My system blows up!! Returned to the Topology stage and rebuilt my system ensuring that I followed the procedure correctly for the InflateGro process. It appears to be correct, rea

Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault

Steve Vivian wrote: New to Gromacs. Worked my way through the tutorial with relatively few issues until the Equilibration stage. My system blows up!! Returned to the Topology stage and rebuilt my system ensuring that I followed the procedure correctly for the InflateGro process. It appe