[gmx-users] REST2 with gromacs-4.5.5 plumed2.2.0 -hrex

Saravanan msrvnn+gmx at gmail.com
Thu Mar 6 11:53:19 CET 2014

Hi All,

I am running into a few problems trying to do REST2 using the version of
plumed available at github.com/GiovanniBussi/plumed2/tree/v2.0-hrex.

I have successfully patched gromacs-4.5.5 with plumed downloaded from the
link and when I run "mdrun_mpi -h" the "-plumed" option is properly
displayed. Later I prepared a simulation with a small protein marking all
of the protein atoms as hot atoms ( with _ tag ) in the processed.top file.
The temperature range selected was from 300 to 500 and I used the script
mentioned in hrex.txt for generating topol$i.top files for 8 replicas. At
this point, I was confused as to how the .mdp files for the different
replicas should contain.

When I kept the temperature for all the replicas at 300 (Assuming that
temperature is taken care by lambda scaling of the parameters in the .top
files). I ran mdrun_mpi with the -hrex flag but it returns me the following
exchange probability

Replica exchange at step 250 time 0.5
  dplumed =  0.000e+00  d =  0.000e+00Repl 0 <-> 1  dE =  0.000e+00  dpV =
 0.000e+00  d =  0.000e+00
Repl ex  0 x  1    2 x  3    4 x  5    6 x  7
Repl pr   1.0       1.0       1.0       1.0

Looks like the replica exchange probability is taken as 1.0. Is it because
all the temperatures are the same in the .mdp files? It doesnt return any
error message regarding this as well.

Please help me identify the problem.


Saravanan Murugeson
Graduate Student
Lab-2, Department of Biological sciences and Bio-engineering,
Indian Institute of Technology Kanpur

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