----- Original Message ----- From: David de Sancho <daviddesan...@gmail.com> Date: Wednesday, September 8, 2010 8:04 Subject: [gmx-users] Re: Restarts: Truncation of file *.xtc failed To: gmx-users@gromacs.org
> Hi > Thanks Greg for your answer. > Yes, my simulation is in fact pretty long and its files are considerably > large. The size of the xtc files is approximately ~2 GB when I am trying to > do the restart. > I thought on the contrary that my problem was related to another post in > today's list > (http://lists.gromacs.org/pipermail/gmx-users/2010-September/053701.html). My > xtc files were not synchronized (by very little). The answer to that other > message was that in case the xtc files were not synchronized one would have > to create new and synchronized tpr files using tpbconv and the trr files with > positions and velocities. 4.0.x would write checkpoint files for REMD out of sync under some circumstances. One approach is to truncate all the files to a time when you have a checkpoint available for all replicas. Another would be to take the .tpr and .cpt for each replica on its own, adjust the final timestep with tpbconv so that you can synchronise each replica in a single-replica simulation, simulate, and once everything's in sync, restart REMD. Mark
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