[gmx-users] REMD Showing Zero Exchange Probability
Smith, Micholas D.
smithmd at ornl.gov
Fri Jul 20 14:04:57 CEST 2018
How frequently are you trying to exchange?
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Ligesh Lichu <lichuligesh at gmail.com>
Sent: Friday, July 20, 2018 4:39 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] REMD Showing Zero Exchange Probability
I have performed REMD for a system containing Protein, Reline, Urea and
Water in the temperature range 290 to 450 K consist of 16 replicas out of
47 replicas generated by REMD temperature generator. But after the MD
simulation the exchange probability is zero. I have used position
restraints for reline, urea and protein. Is there any chance that position
restraints cause the exchange probability to be zero? I have one more
query that, the REMD temperature generator produced around 45 to 54
replicas for my system in the required temperature range. But I have only
80 processors to do the job, So is it necessary to choose the consecutive
temperature replicas given by the REMD temperature generator or I can skip
some temperatures in between?
If I am using the equation *Ti = T0 exp (k* i)*, what determines the value
of 'k' how it affects the exchange probability? How can I choose the value
of 'k' for an arbitrary system?
Thanks in advance...
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