[gmx-users] Questions regarding REMD Statistics

Kong xq xqkong776 at gmail.com
Sun May 5 03:39:04 CEST 2013

Dear GMX users,

    I have some concerns about the statistics analysis of REMD which do
need your generous help.

    I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas
spaning from 300K to 390K. Then I want to do some statistics analysis for
the results. First, I calculated the acceptance ratio for the adjacent
pairs of temperatures (showing below). It seems that most of the values are
uniform ( 0.25 +/- 0.11) . Second, I  followed the track of replica 1 in
the temperature space with the information from replica_temp.xvg  generated
by demux.pl(demux.pl md0.log) scipt. However, the histogram(table below)
indicated that the distribution of replica 1 in temperature space is not
very uniform. So my question is why did the nonuniform temperature
distribution of replica 1 occur given the fact that the acceptance ratio
indicated a free random walk in temperature space ? What's more, whether a
longer simulation was needed to make a more flatter temperature
distribution for each replica?

    By the way, I want to double check that each column except the first in
replica_temp.xvg represents a constant temperature corresponding to that
specified in tpr file, we may need to follow the replica index (such as 0
for the first replica) among different coloumns (or temperatures). Does
this make sense?

   Best regards!

   Xiangqian Kong

*The frequency of replica 1 in temperature space *
  Temperature Frequency  310 16.91%  320 11.58%  330 13.68%  340 13.79%  350
12.64%  360 11.60%  370 4.38%  380 5.26%  390 10.16%

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