[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
LM
-----------------------------------------------------------------------------
Luca Mollica
ZRL-IBM Research Center
Saumerstrasse 4
8803, Rueschlikon (Zurich)
CH
Tel: 0041 - 447248217
email: YLU at zurich.ibm.com
email(alt): ZRLYLU at ch.ibm.com
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