Re: [gmx-users] mdrun error

Mark thanks for your reply and support . [?] Regards Lovika On Sat, May 17, 2014 at 5:23 PM, Mark Abraham wrote: > No, the .mdp file mostly describes your model physics (but there are some > implementation details that affect parallelization in there). > > Your GROMACS CMake configuration, mdru

Re: [gmx-users] translational dipole moment during the simulation

I can't help with the source code modification, and I am surprised that you actually need 5 fs resolution, but if you are simply having trouble with disk space, you could set up a loop inside your job script that (a) runs mdrun, (b) extracts velocities, (c) makes a copy of the raw output, saving

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote: Dear Mark, I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. There are two possibilities: 1. You built the system wrong and trjconv can't fix it. Without the full sequence of commands used to build the system, no one can p

[gmx-users] translational dipole moment during the simulation

Hello, I am calculating rotational and translational part of dipole moment. For translational dipole moment I want to save the velocities each 5fs and for rotational part I want to update trajectory each 2ps. I am running 30ns simulation. The size of trajectory is big and simulation get crashed be

Re: [gmx-users] mdrun error

No, the .mdp file mostly describes your model physics (but there are some implementation details that affect parallelization in there). Your GROMACS CMake configuration, mdrun command line and the attributes of your hardware are the biggest factors that determine how mdrun will try to parallelise.

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

Dear Mark, I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. Juan C. > > Dear Justin, > > thank you. I’ve tried the following but neither of them worked, I get the same result. > > trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact > > trjcon

Re: [gmx-users] mdrun error

Thanks for quick reply Mark...what information you are asking for?Should I search for this my .mdp file?? Thanks Lovika On Sat, May 17, 2014 at 11:35 AM, Mark Abraham wrote: > Your simulation seems too small to parallelize in the way you/mdrun tried. > But we need more information to be sure.