On 24/09/2012 4:49 PM, Andreas Zink wrote:
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
trajectory.
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"?
IIRC trjcat is reasonably sophisticated about making sure it skips both
exchange attempts between output steps and vice-versa. I suggest you
make yourself a toy case exchanging every 10 steps and saving every 100
steps and observe the behaviour of trjcat. Please report back with your
observations so others can learn :-)
Mark
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