[gmx-users] Changing cos_acceleration

Hello, I am working with a DPPC lipid bilayer system in water, and I would like to add a shear force to the bilayer. Preferably, this force would be a function of the z coordinate and be maximal at the bilayer surface and decay to zero at the box top and bottom. For this, I have been looking

Re: [gmx-users] soft-core potential in combination with PME

Hi David and all, Tanks for your elaboration on the subject. I've done a couple of free energy simulations myself, also on disappearing charged atoms, but so far I've not yet encountered any of the instability problems you mention here (though I did encounter instabilities at high lamda values

Re: [gmx-users] Preliminary report on benchmark on Opteron Cluster Infiniband on current CVS version

Erik Lindahl wrote: Hi, On Apr 17, 2007, at 6:26 PM, Luca Ferraro wrote: /usr/bin/time mpiexec -n ${proc} mdrun_mpi -d 1 ${proc} 1 For a start, the domain decomposition flag is "-dd" :-) Cheers, In addition you should add the -dlb flag for load balancing. -- David.

Re: [gmx-users] Preliminary report on benchmark on Opteron Cluster Infiniband on current CVS version

Hi, On Tuesday, 17. April 2007 18:26, Luca Ferraro wrote: > Hello GROMACS world, > > I would like to report a little benchmark activity within some > preliminary results I recently performed on two different cluster > (Opteron-SC and Opteron-DC on InfiniBand) using the current CVS version > of GRO

Re: [gmx-users] Preliminary report on benchmark on Opteron Cluster Infiniband on current CVS version

Hi, On Apr 17, 2007, at 6:26 PM, Luca Ferraro wrote: /usr/bin/time mpiexec -n ${proc} mdrun_mpi -d 1 ${proc} 1 For a start, the domain decomposition flag is "-dd" :-) Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www

[gmx-users] Preliminary report on benchmark on Opteron Cluster Infiniband on current CVS version

Hello GROMACS world, I would like to report a little benchmark activity within some preliminary results I recently performed on two different cluster (Opteron-SC and Opteron-DC on InfiniBand) using the current CVS version of GROMACS. From these preliminary tests, it seems that the speedup and

Re: [gmx-users] on NVE and pressure

From: lorix <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] on NVE and pressure Date: Mon, 16 Apr 2007 15:33:04 +0200 The goal of mine is to see whether I can simulate a large conformational change on an protei

Re: [gmx-users] UNABLE TO GENERATE TOPOLOGY

Hi try this command pdb2gmx -f Fe.pdb -p Fe.top Regards Robert > Hi ! can anyone help? > how can I generate a topology file a single atom "Fe" for use in gromacs. > > Thanks in advance, > --Subhrangshu > ___ > gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] UNABLE TO GENERATE TOPOLOGY

Hi Subhrangshu, See chapter 5 of the manual. Something like: #include "ffforcefieldofyourchoice.itp" #include "ions.itp" [ system ] A single Fe [ molecules ] FE 1 Best, Tsjerk On 4/17/07, Subhrangshu Supakar <[EMAIL PROTECTED]> wrote: Hi ! can anyone help? how can I generate a topol

[gmx-users] UNABLE TO GENERATE TOPOLOGY

Hi ! can anyone help? how can I generate a topology file a single atom "Fe" for use in gromacs. Thanks in advance, --Subhrangshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arch