sarbani chattopadhyay wrote:
Hi,
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 ?
yes.
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?
yes.
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?
yes.
you can verify this by plotting e.g. RMSD as a function of time for each
replica, these should be continuous functions of time, even at exchange
times.
It will be of great help if I get any suggestions regarding my queries.
Thanking You,
Sarbani
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