[gmx-users] problem implementing REST2 in GROMACS 4.6.5

Mark Abraham mark.j.abraham at gmail.com
Mon Sep 14 12:48:47 CEST 2015


The mdrun .log file should be emitting the same energy values on the two
replicas as are used in the exchange attempt. Is that what you are
comparing when you say "I have also calculated..." If mdrun's potential
energy output is the same on each replica, then the problem likely lies
with your implementation of scaling.


On Mon, Sep 14, 2015 at 12:26 PM Elio Fiorentini <
elio.fiorentini90 at gmail.com> wrote:

> 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,
> 2010).
> 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.
> Best,
> --
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