[gmx-users] g_msd, REMD, trestart...

Mark Abraham Mark.Abraham at anu.edu.au
Sat Mar 15 00:52:00 CET 2008

Julián GC wrote:
> Hi all,
> I'm studying small water clusters with Gromacs 3.3 (I'm also performing 
> MC with a self-writed MC program).
> I run 24 boxes in paralell, with -replex 100000 (it is important to use 
> replica exchange).
> I need to get MSD results, but I don't think g_msd takes into account 
> that every 100ps the boxes are being exchanged.

Constant-T REMD trajectories are intrinsically discontinuous, so g_msd 
will also have discontinuities. If all of your replicas started from the 
same structure, then the MSD calculation is measuring from the same 
starting point. If you need statistics for longer continuous chunks, 
then you need to reconsider your approach. If you can adjust suitably 
for temperature, then generating demux-ed constant-replica REMD 
trajectories will at least eliminate the discontinuities. (demux.pl is 
either in the source distribution or on the contributions section of the 
GROMACS webpage, I forget which)

> Does anyone knows how to fix that? Have anyone had to deal with 
> something like this before?
> (The obvious "easy" solution is to chop the trajectory in blocks of 
> 100ps, calculate MSD in each block, and then average all the results, 
> but would be nice if this annoying "shortcut" could be avoided)

See g_msd -h... I think -trestart saves you some legwork here.


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