[gmx-users] understanding the output of REMD

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 28 03:38:06 CEST 2011



sreelakshmi ramesh wrote:
> demultiplex script was used to gave one log file of one replica as  the 
> input like perl demux.pl <http://demux.pl> md0.log it gave two output files.
> 
> |replica_index.xvg| and replica_temp.xvg.
> 
> 
> the file replica_temp looks like this
> 0           0    1    2    3    4    5    6    7
> 2           0    1    2    3    4    5    7    6
> 4           0    1    2    3    4    5    7    6
> 6           0    1    2    3    5    4    6    7
> 8           0    1    2    3    5    4    6    7
> 10          0    1    2    3    5    4    6    7
> 12          0    1    2    4    5    3    6    7
> 14          0    1    2    4    5    3    6    7
> 16          0    1    2    3    5    4    6    7
> 18          0    1    2    3    5    4    7    6
> 20          0    1    2    3    5    4    7    6
> 22          0    1    2    3    5    4    7    6
> 24          0    1    2    3    5    4    7    6
> 26          0    1    2    3    5    4    6    7
> 28          0    1    2    3    5    4    6    7
> 30          0    1    2    3    5    4    6    7
> 32          0    1    2    3    5    4    6    7
> 34          0    1    2    3    5    4    6    7
> 
> 
> the other index file was passed over trjcat and i concatenated all the 
> other trajectories like this
> 
> trjcat  -f *.trr  -demux replica_index.xvg -o final.trr
> 
> now how to produce temp evolution over time with these concatenated 
> trajectories
> 

You now have all the information you need.  In replica_temp.xvg, you can follow 
each simulation (by its index) as it moves between all of the ensembles.  If you 
extract the temperatures from each .edr file over time, you can then map which 
replica index occupied that ensemble at the given time.  There are no Gromacs 
tools to do this; it will require some rather simple scripting to pull the 
information from the text files.

-Justin

> thanks in advance,
> sree.
> 
> On Thu, Jul 28, 2011 at 6:53 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     sreelakshmi ramesh wrote:
> 
>         after having enough exchanges how to follow the temp trajectory
>         of each replica in REMD ? I tried to make it out from edr file
>         of each replica.looks like replica at a particular temp remains
>         almost at a same temp throughout the simulation and does not
>         visit all the other tempratures.any help please.
> 
> 
> 
>     Trajectories and energy files are ensemble-continuous.  Use the
>     demux.pl <http://demux.pl> script to demultiplex the trajectories
>     and produce temperature evolution over time.
> 
>     -Justin
> 
>         Regards,
>         sree.
> 
> 
>         On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            sreelakshmi ramesh wrote:
> 
>                dear all ,
>                I am new to ReMD simulations.And i done a trial run of 100 ps
>                for 7 replicas . if i view the log file for output i get
>                something like this for every replica
>                for one of the replica the log file looks like this
> 
>                Replica exchange at step 1000 time 2
>                Repl 0 <-> 1  dE =  6.793e+02  dpV =  0.000e+00  d =
>          6.793e+02
>                Repl ex  0    1    2    3    4    5    6
>                Repl pr   .00       .00       .00    Replica exchange at step
>                2000 time 4
>                Repl ex  0    1    2    3    4    5    6
>                Repl pr        .00       .00       .00
>                Replica exchange at step 3000 time 6
>                Repl 0 <-> 1  dE =  6.790e+02  dpV =  0.000e+00  d =
>          6.790e+02
>                Repl ex  0    1    2    3    4    5    6
>                Repl pr   .00       .00       .00    Replica exchange at step
>                4000 time 8
>                Repl ex  0    1    2    3    4    5    6
>                Repl pr        .00       .00       .00
>                Replica exchange at step 5000 time 10
>                Repl 0 <-> 1  dE =  6.874e+02  dpV =  0.000e+00  d =
>          6.874e+02
>                Repl ex  0    1    2    3    4    5    6
>                Repl pr   .00       .00       .00    Replica exchange at step
>                6000 time 12
>                Repl ex  0    1    2    3    4    5    6
>                Repl pr        .00       .00       .00
>                Replica exchange at step 7000 time 14
>                Repl 0 <-> 1  dE =  6.535e+02  dpV =  0.000e+00  d =
>          6.535e+02
>                Repl ex  0    1    2    3    4    5    6
>                Repl pr   .00       .00       .00            i had
>         attached only  few lines of log file.can any one tel me
>                how to understand the output.
> 
> 
>            I assume you've seen the following?
> 
>          
>          http://www.gromacs.org/____Documentation/How-tos/REMD#____Understanding_REMD-related_____Output
>         <http://www.gromacs.org/__Documentation/How-tos/REMD#__Understanding_REMD-related___Output>
>          
>          <http://www.gromacs.org/__Documentation/How-tos/REMD#__Understanding_REMD-related___Output
>         <http://www.gromacs.org/Documentation/How-tos/REMD#Understanding_REMD-related_Output>>
> 
>            Listed are the exchange probabilities between neighboring
>         replicas.
>             Your results indicate that your systems are not exchanging (e.g.
>            probability is zero).
> 
>            -Justin
> 
>            --     ==============================____==========
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>            <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
> 
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>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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