Re: [gmx-users] new forcefield not appear in slave node pdb2gmx list

This could be helpful, I hope. http://www.gromacs.org/Documentation/File_Formats/FF.dat?highlight=change+ff+list   Dra.M.Florencia Martini Cátedra de Farmacotecnia II Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junín 956 6º (1113) TE: 54 011 4964-8273

Re: [gmx-users] RMSD

The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1 refers time, and it is because you do not have a trajectory. You are comparing only two .pdb structures, so it is consistent that you obtain only one value, as you do not have more than one frame to compare. Regards Flor  

Re: [gmx-users] merge many boxes

You should try packmol software. You will need to use a pdb formats, but then you transform to .gro with pdb2gmx. It´s free and very easy to use. http://www.ime.unicamp.br/~martinez/packmol/ Flor   Dra.M.Florencia Martini Cátedra de Farmacotecnia II Facultad de Farmacia y Bioquímica

Re: [gmx-users] PEO and OPLS-AA FF in gmx

Perhaps you can do your parametrization. Enter to the prodrg page and you will see! The page is: http://davapc1.bioch.dundee.ac.uk/prodrg/ and you will get your .gro and .top, and you don't need to use the pdb2gmx. If you want to use it anyway, you need to edit the data base, but I think that

Re: [gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4

is your performance on a single node (4 CPUs)? You could compare that to the performance of 4 CPUs on 2 nodes to determine the networkimpact. Carsten On Sep 24, 2009, at 5:08 PM, FLOR MARTINI wrote: Thanks for your question. We are running a lipid bilayer of 128 DPPC and 3655 water molecules

[gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4

hi,    We are about to start running GROMACS 4.0.4 with OpenMPI, in 8 nodes, quad core Rocks cluster. We made some tests, without PME and found two notable things: * We are getting the best speedup (6) with 2 nodes ( == 8 cores ). I read the Speeding Up Parallel GROMACS in High Latency networks

RE: [gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4

Thanks for your question. We are running a lipid bilayer of 128 DPPC and 3655 water molecules and the nstep of the mdp is a total for 10 ns. I don´t think really that our system is a small one... Dra.M.Florencia Martini Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas Cátedra