[AMBER] About T-REMD convergence

From: Francesco Pietra <chiendarret.gmail.com>
Date: Mon, 16 Sep 2013 11:17:24 +0200

 As to

From: Carlos Simmerling

Date: Tue, 18 May 2010 06:54:14 -0400
 Much depends on the initial structures. If all the same, you realy
need a second run from different coordinates. If different, the data
from all replicas should match. This means that you can extract the
temperature data from each replica and they should match. For example,
fraction folded at 300k must be the same for replica 1 and 2. This
takes some effort to analyze.

I assume that for a 32-replicas T-remd in the 314-600K range, the above
criterion should be applied at replicas sorted at 314K, if the interest is
in the system at 314K. Replicas extracted at all other temperatures should
simply be neglected?

I started such a T-remd under GB conditions (abandoning implicit water
after Prof Simmerling 2013 paper) and progressively increasing temperature
for a 34aa peptide under restraining of dihedrals for a short initial
stretch (the only portion diffracting enough under X-ray). Debug T-remd
with 32 replicas and 3700 steps for each replica at ts=0.2 fs (exchange
ratio higher than 0.7), thus all rigid bonds, show better folding at 600K
than 314K. Although the conformation is unknown, there is a more ordered
organization ant 600 than 314K. Is that acceptable in order to go to

Good exchange (ratio 0.4) also with 16 replicas, however with very little
gain of computer time as I am bound to use 64 nodes.

All rigid bonds is something that for MD in general I dislike, particularly
if moving ligands are under scrutiny. What about for such a type of T-remd?

Thanks so much for advice
francesco pietra
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Received on Mon Sep 16 2013 - 02:30:02 PDT
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