[gmx-users] Fast exchanges for REMD

Andreas Zink zinkandi at googlemail.com
Mon Sep 24 08:49:57 CEST 2012

Dear all,

I've done some REMD simulations using a quite high exchange attempt 
frequency (10 attempts per ps) as proposed by Sindhikara et al. 
("Exchange Often and Properly in Replica Exchange Molecular Dynamics",J. 
Chem. Theory Comput. 2010, 6, 2804–2808 ).
Unfortunately, I have now recognized that the demux perl script cannot 
account for an EAF which is higher than the saving frequency in the 

Comments from demux.pl:
# If your exchange was every N ps and you saved every M ps you can make for
# the missing frames by setting extra to (N/M - 1). If N/M is not integer,
# you're out of luck and you will not be able to demux your trajectories 
at all.

In my case exchanges every 0.1 ps and saved every 5 ps

Changing the demux.pl script, so that it writes the "replica_index.xvg" 
with a higher precision (time in ps) should be no problem. However, my 
question is: will this work together with trjcat? Does trjcat search for 
the timeframe given in the first column of "replica_index.xvg", or does 
it links each line to one saved timeframe? If so, could I just delete 
the additional lines in "replica_index.xvg"?

I would be really happy if someone could help me with this!


More information about the gromacs.org_gmx-users mailing list