Dear all,
I could finally demux my REMD trajectories with high EAF. They look
fine, but I'm not 100% sure about it.
Unfortunately, there seems to be a "bug" in mdrun. As you migh know, the
log files contain the exchange attempts like:
Replica exchange at step 2000 time 4
Repl ex 0 1 2 3 x 4 5
Repl pr .00 1.0
However, the time value (4 in this example) is limited to 6 digits. It's
not really a bug because I think GROMACS recommends EAFs of max. 1/ps.
But if you exchange every 0.5 ps (EAF= 2/ps) you can run the simulation
for max. 99999 ps only. Otherwise your log will simply chop the time
after the decimal point, e.g.
Replica exchange at step ... time 99999.5
...
Replica exchange at step ... time 100000
...
Replica exchange at step ... time 100000
...
Replica exchange at step ... time 100001
...
I have written a Perl script which fixes the time values, based on the given
number of steps and stepsize. Additionally the demux.pl script was changed
because it also chops after 6 digits. I simply changed:
printf(NDX "%-20g",$t);
in the "pr_order" and "pr_revorder" subroutines to:
printf(NDX "%-20.2f",$t);
and it works just fine.
Like I said the trajectories look fine, but I'm not really sure if it's
actually correct that way. I would be happy if anyone would like to discuss
this :)
Cheers,
Andi
Am 24.09.2012 08:49, schrieb Andreas Zink:
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"?
I would be really happy if someone could help me with this!
Thanks!
Andi
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