<P>
Hi,<BR>
I have few queries regarding Replica Exchange MD.<BR>
<BR>
1) I have 17 replicas , and the files are named as md_0.trr,......,.md_16.trr.Replica exchange <BR>
is attempted every 100ps.<BR>
Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written in <BR>
md_0.trr files corresspond to the simulation at the lowest temperature say 313K. At 100ps, <BR>
if there is a successful exchange between replica 0 and 1, then the coordinates and boxes <BR>
are exchanged and the coordinates,etc. of replica 1 at 100 ps are written in md_0.trr files.<BR>
Have I understood the process correctly ?<BR>
<BR>
2) Once the simulation is over I have to use demux.pl to get the replica_index.xvg and replica_temp.xvg file.<BR>
The replica_temp.xvg file has 18 columns, the first one being the time and 17 columns. <BR>
Thus the 2nd column gives me the record regarding which replica occupies the lowest temp. ie. 313 K every 100ps.<BR>
Is this correct?<BR>
3) Using replica_index. xvg , I will have to use "trjcat" to make the trajectories continous.<BR>
when I give the command-> " trjcat -f md_*.trr -demux replica_index.xvg ",it attempts to <BR>
write just one file "trajout.xtc" and gives a bus error.<BR>
But i give the command <BR>
trjcat -f md_*.trr -demux replica_index.xvg -o new_md_0.trr new_md_1.trr ......new_md_16.trr<BR>
,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?<BR>
<BR>
It will be of great help if I get any suggestions regarding my queries.<BR>
Thanking You,<BR>
Sarbani<BR>
<BR>
</P>
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