[gmx-users] understanding the output of REMD

[sreelakshmi ramesh]

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.


Regards,
sree.

On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul <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>
>
> 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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110728/723af22b/attachment.html>