[gmx-users] questions regarding Replica Exchange
David van der Spoel
spoel at xray.bmc.uu.se
Fri Apr 10 09:21:42 CEST 2009
sarbani chattopadhyay wrote:
> 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?
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
> It will be of great help if I get any suggestions regarding my queries.
> Thanking You,
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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