[gmx-users] questions regarding Replica Exchange

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Fri Apr 10 09:12:34 CEST 2009

    I have few queries regarding Replica Exchange MD.

1) I have 17 replicas , and the files are named as md_0.trr,......,.md_16.trr.Replica exchange 
is attempted every 100ps.
Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written in 
md_0.trr files corresspond to the simulation at the lowest temperature say 313K. At 100ps, 
if there is a successful exchange between replica 0 and 1, then the coordinates and boxes 
are exchanged and the coordinates,etc. of replica 1 at 100 ps are written in md_0.trr files.
 Have I understood the process correctly ?

2) Once the simulation is over I have to use demux.pl to get the replica_index.xvg and replica_temp.xvg file.
The replica_temp.xvg file has 18 columns, the first one being the time and 17 columns. 
Thus the 2nd column gives me the record regarding which replica occupies the lowest temp. ie. 313 K every 100ps.
Is this correct?
3) Using replica_index. xvg , I will have to use "trjcat" to make the trajectories continous.
when I give the command-> " trjcat -f md_*.trr -demux replica_index.xvg ",it attempts to 
write just one file "trajout.xtc" and gives a bus error.
But i give the command 
 trjcat -f md_*.trr -demux replica_index.xvg -o new_md_0.trr         new_md_1.trr ......new_md_16.trr
,the command runs fine.  What coordinates are written in the new_md_0.trr( ie. the new continous trajectory file) ? Does this continous file contain the information about the replica 0 over the time?

It will be of great help if I get any suggestions regarding my queries.
Thanking You,

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