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.gup...@gmail.com
shubhangi_gu...@iitb.ac.in
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