[gmx-users] REMD, broken simulations and analysis

Luca Mollica YLU at zurich.ibm.com
Fri Oct 21 15:36:39 CEST 2005

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 ?

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 ? 

Thanx a lot




Luca Mollica
ZRL-IBM Research Center
Saumerstrasse 4
8803, Rueschlikon (Zurich)

Tel: 0041 - 447248217

email:        YLU at zurich.ibm.com 
email(alt): ZRLYLU at ch.ibm.com 
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