[gmx-users] Varying exchange probabilities between replicas in REMD
mark.j.abraham at gmail.com
Sat Jul 21 17:19:26 CEST 2018
It won't be constant. There's quite some literature on the topic. In
general you can't predict the probability, nor how the replicas are best
On Sat, Jul 21, 2018, 15:11 Shubhangi Gupta <ignahbuhs.gupta6 at gmail.com>
> Hello all,
> I am trying to do REMD simulation following the methodology
> given by Mark Abraham (
> My system is a small 34 residue protein in explicit water. I have generated
> temperatures using the server *http://folding.bmc.uu.se/remd/
> <http://folding.bmc.uu.se/remd/>*, keeping the exchange probability
> constant at 0.2. The smallest temperature is 280K and highest temperature
> is 380K. I obtained a total of 20 replicas. However, the log file shows
> replica exchange statistics with average exchange probabilities varying
> from 0.03 to 0.28. The smaller values are for exchanges between higher
> temperature replicas.
> I have also tried to reproduce simulations from an old paper which has used
> AMBER software, using the temperatures mentioned there. It is for a 35
> residue protein in implicit water. The exchange probabilities vary from
> 0.32 to 0.72 when I am trying this in GROMACS.
> As I understand the exchange probabilities should be nearly constant. Can
> someone please help me with this. Any help is appreciated.
> Shubhangi Gupta
> PhD Research Scholar (YUS lab)
> Dept of Chemistry
> Indian Institute of Technology Bombay
> Powai, Mumbai-400076.
> e-mail ID: ignahbuhs.gupta6 at gmail.com
> shubhangi_gupta at iitb.ac.in
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