[gmx-users] problem implementing REST2 in GROMACS 4.6.5

Elio Fiorentini elio.fiorentini90 at gmail.com
Mon Sep 14 12:26:11 CEST 2015

Dear gromacs users :

I am trying to implement REST2 in gromacs following the procedure proposed
by Tsuyoshu Terekawa  ( On easy implementation of a variant of the replica
exchange with solute tempering in GROMACS, J Comput Chem. 32, 1228-1234,
Thus, I have changed the file ffnonbonded.itp and ffbonded.itp, scaling the
charges by the square root of gamma ( where gamma is the ratio between
T_low and T_high ) and the spring constants of the solute by gamma.
I did a short test with a segment of 18 residues using 12 replicas and in
the md"i".log files ( where 'i' stand for 0 ... 11 ), I found that the term
'Repl 0<->1 dE = 0.000e+00', all with the value 0 and consequently the
exchange probability of two replicas is 1.0. This happens for each replica.
I have also calculated the energy differences for these replicas and found
that they were not zero. I wonder what the problem is, in this case.
Could anyone help me solve the problem? Thanks in advance for any help on
this matter.

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