[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:
>   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 ?

> 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,
> Sarbani
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list