[gmx-users] translational dipole moment during the simulation

Christopher Neale chris.neale at alum.utoronto.ca
Sun May 18 00:49:25 CEST 2014

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 less frequently, (d) delete the original, very frequent output files, (e) repeat the loop while loading in a checkpoint file in mdrun. However, before launching into this, I would check that saving the output every 5 fs is not drastically reducing your simulation speed. If it is killing your throughput to save every 5 fs (I presume that it is), and if you really need 5 fs resolution, then you'll likely need to get additional help on modifying the source code.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nilesh Dhumal <ndhumal at andrew.cmu.edu>
Sent: 17 May 2014 13:46
To: gmx-users at gromacs.org
Subject: [gmx-users] translational dipole moment during the simulation


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
because of less space.

Could it possible to print only velocity at the center at each 5 fs?

I am thinking to calculate the velocity at the center and the change
during the simulation. How difficult  to make this change in the code?


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