[gmx-users] REMD, broken simulations and analysis

Xavier Periole x.periole at rug.nl
Fri Oct 21 15:48:08 CEST 2005

Luca Mollica wrote:

> Dear users,
> I am experiencing the REMD options of mdrun for the GMX 3.3 version on 
> a system with 26 replicas, with a protein, water and ions:
> I have to say that it works pretty well and it is really easy going to 
> set upa REMD simulation with these new mdrun flags.
> But I have a couple of questions about it before finishing a 
> nanosecond simulation and starting to analyze it.
> 1.  Due to maintenance operations on the cluster onto wich REMD is 
> running, the simulation has been interrupted, and I have made it 
> restarting using the tpbconv command like in ordinary  
>  simulations: is there any consequence on the reliabiliy of Replica 
> Exchange method applications in this case ? does the tpbconv command 
> works correctly in this case ? Or does it have any different usage mode ?
I don't know how it is implemented but you certainly going to face the 
same probleme that I got
with another version. The problem is that the replicas are followed by a 
number given at the
beginning of the simulation are related the the inital tmperature. This 
is reassigned within the new
tpr files ... be aware of this for the analysis later ...

You also should check whether the same amount of trajectories was 
written in the 26 trr files.]
That would be not nice to restart the simulations a different times ...

> 2. After the end of the simulations, what do I have in my hand ? I can 
> see my working directory full of as many trajectories and log and 
> energy files as the number of replica I have for my systems: the log 
> files tell me when there happened to be an exchange between replicas, 
> but what does the trajectory file represents exactly ? Is it the 
> trajectory of replicas across temperature space or is it a collection 
> of states at a certain temperature ?

I think the trajectories are written by temperatures ... should be a 
utility allowing to create trajectories
of one replica walking inthe temperature space ...


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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