[gmx-users] Fast exchanges for REMD

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 25 00:44:11 CEST 2012

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 :-)


More information about the gromacs.org_gmx-users mailing list