Re: [gmx-users] tesla vs gtx

Hi, Teslas should be superior when it comes to reliability, but otherwise, for Gromacs 4.6 GeForce cards are perfectly fine and no Tesla-specific features will provide performance benefits. The only exception is GPUDirect for InfiniBand which might not work with consumer boards -- , although I don

[gmx-users] strange problem with performance information

Hi: I am using the following command to submit gromacs md jobs in cluster: mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v -s nvt.tpr" -mode VN -np 128 Then I use command tail -f gromacs.out to check the performance of my jobs and I get the following information:

Re: [gmx-users] strange problem with performance information

On 6/01/2012 2:00 AM, Albert wrote: Hi: I am using the following command to submit gromacs md jobs in cluster: mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v -s nvt.tpr" -mode VN -np 128 Then I use command tail -f gromacs.out to check the performance of my jobs a

[gmx-users] Cytochrom C

Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? Thanks, Dariush -- 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 befor

Re: [gmx-users] Cytochrom C

Have you try www.pdb.org? http://www.pdb.org/pdb/explore/explore.do?structureId=3cyt Nuno On Thu, Jan 5, 2012 at 4:40 PM, Dariush Mohammadyani < d.mohammady...@gmail.com> wrote: > > Hi all, > > Has anybody made initial configuration for Cytochrom C? Can it be shared > with me? > > Thanks, > Dar

Re: [gmx-users] Cytochrom C

Dariush Mohammadyani wrote: Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? There are several in the PDB. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Departmen

Re: [gmx-users] Cytochrom C

Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know which forcefield is proper to use. I also tried MARTINI force field according their website; I used m

Re: [gmx-users] Cytochrom C

HEME is in the charmm27 force field. bob h. On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know

[gmx-users] decoupling a group of a molecule

Hello, Does anybody know how to do the same decoupling technique from Justin's tutorial but only for a small piece of a molecule rather than the entire molecule? Is it simply writing on the topology B state as zero charge and then mutating to a dummy atom? Thanks. -- Best regards, Fabian F. C

Re: [gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5

On 5/01/2012 3:37 AM, Rashek Kazi wrote: Dear Mark (and all), Yes the issue for me turned out to be the version of FFTW I was using. The installation instructions must be different for the most recent FFTW-3.3 build but I lack the programming knowledge to know how to make this work. I rathe

[gmx-users] GROMACS mpispawn error

Hi all, I run into this error when I was trying to run the simulations. I attached the mdp file I was using. I appreciate it if you could help me to figure it out. mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE Thank you very much. Chelsea 31GCD.

Re: [gmx-users] GROMACS mpispawn error

On 6/01/2012 2:56 PM, Chelsea wrote: Hi all, I run into this error when I was trying to run the simulations. I attached the mdp file I was using. I appreciate it if you could help me to figure it out. mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DO

[gmx-users] another question about performance

Hello: here is my log file for mdrun: Writing final coordinates. step 10, remaining runtime: 0 s Average load imbalance: 10.8 % Part of the total run time spent waiting due to load imbalance: 4.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 19 % Z

Re: [gmx-users] another question about performance

Albert wrote: Hello: here is my log file for mdrun: Writing final coordinates. step 10, remaining runtime: 0 s Average load imbalance: 10.8 % Part of the total run time spent waiting due to load imbalance: 4.3 % Steps where the load balancing was limited by -rdd, -rcon

RE: [gmx-users] another question about performance

Recheck the units for that last number …. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only to

[gmx-users] nodes error

Hello: I found that each time I would like to increase my nodes for MD run, my job always failed. it said: Will use 192 particle-particle and 64 PME only nodes This is a guess, check the performance at the end of the log file --- Program md

Re: [gmx-users] nodes error

Hi, You should start from here: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm Terry On Fri, Jan 6, 2012 at 12:49 PM, Albert wrote: > Hello: > I found that each time I would lik

[gmx-users] NPT error

Hi: I am following the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html the nvt step goes well, but the NPT always doesn't work. it said: Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fat

[gmx-users] [~solved] Force field for polymer molecule - tips

Dear all, In December 2011 I was asking about tips on how to port a Charmm generalized forcefield for a polymer to Gromacs. I am happy to report that the forcefield was ported to Gromacs in a way that allows the use of pdb2mx in order to create an initial topology and .gro file. Major lesso

[gmx-users] Re: nodes error

thank you very much for kind reply. I change my command as following: mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v -s npt.tpr -nt 1" -mode VN -np 256 the "-nt 1" option has been added above. but it still doesn't work and here is the log file Initializing Dom

Re: [gmx-users] Re: nodes error

"The minimum cell size is controlled by the size of the largest charge group or bonded interaction and the largest of rvdw, rlist and rcoulomb, some other effects of bond constraints, and a safety margin. *Thus it is not possible to run a small simulation with large numbers of processors.*" Based

[gmx-users] tesla vs gtx

Hey, From the previous posts on the list I got the feeling that gtx are fine enough for gromacs calculations and 4 times more expensive teslas are actually not necessary. However the hardware providers discourage us from using gtx in a small cluster. The number of reasons is listed on t

Re: [gmx-users] copper and His residues

Thanks for your help-- 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 before posting! Please don't post (un)subscribe requests to the list. Use the www interface

Re: [gmx-users] how to plot g_msd in one direction?

On 4/01/2012 7:12 PM, Kiwoong Kim wrote: Dear members of gromacs I have several questions. I have been working on the diffusion problem (diffusing particles diffuse into the zeolite). Although I have successfully obtained the output file, there are problems for analyzing it. My questions

[gmx-users] Re: problem of installing gromacs4.5.4

Dear Justin: Thank you very much for your reply, but I have another problem. After I install the fftw package, and remove the argument of the --enable-mpi when installing the gromacs package by using the follow commands: export CPPFLAGS=-I/my_path/ export LDFFLAGS=-L/my_path/ ./configure --pr

Re: [gmx-users] Re: problem of installing gromacs4.5.4

On 6/01/2012 12:37 AM, mirc...@sjtu.edu.cn wrote: > Dear Justin: > > Thank you very much for your reply, but I have another problem. > > After I install the fftw package, and remove the argument of the --enable-mpi > when installing the gromacs package by using the follow commands: > > export CPPF