[gmx-users] Varying exchange probabilities between replicas in REMD

[Mark Abraham]

Hi,

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
placed.

Mark

On Sat, Jul 21, 2018, 15:11 Shubhangi Gupta <ignahbuhs.gupta6 at gmail.com>
wrote:

> Hello all,
>
>             I am trying to do REMD simulation following the methodology
> given by Mark Abraham (
>
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
> ).
> 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.
>
>
> Regards,
> 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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