[gmx-users] REST simulation

[Otto Master]

Dear gromacs users,

Recently I stumbled over following paper:
T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant
of the Replica Exchange with Solute Tempering in GROMACS. Journal of
Computational Chemistry 32 (2011) 1228-1234.

The authors suggested an easy way to run this kind of simulation with
Gromacs, without even changing the code. The only thing that is need, is
the the rescaling of the parameters in the parameter file. Since the
reduction of the replica number is quite appealing to me I wonder which
file I have to change? Actually, I thought of manipulating the .tpr file or
to rescale and creating the force fields for every replicate. Is this
feasible, or is there a better way?

Manipulating the .tpr file could be easier, since it unifies (right?) the
parameters from the different force fields, before sending it to the mdrun
application. But for this I would like to understand the tpr file
first.There are quite a lot of entries and first I try to understand LJ
interactions and how they are defined in this file. I found two entries

LJ14
         functype[154]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00,
c6B= 0.00000000e+00, c12B= 0.00000000e+00
         functype[155]=LJ14, c6A= 4.46680887e-03, c12A= 4.74702711e-06,
c6B= 4.46680887e-03, c12B= 4.74702711e-06

which corresponds to following interactions

      LJ-14:
         nr: 876
         iatoms:
            0 type=154 (LJ14) 0 4
            1 type=155 (LJ14) 0 5

When I tried to calculate the parameters from the combination rules (in
this case Gromos 53A6 force field), I found (the highlighted columns
contain the original parameters for the specific atom groups from the
Gromos  documentation and the calculated value for combining the two
parameters:




sqrt(C6i) (from ff) sqrt(C6j) (from ff) sqrt(C6i)*sqrt(C6j) value from tpr
file  functype[154]=LJ14, c6A= CH3 H 0.09805 0 0 0.00E+00
functype[155]=LJ14, c6A= CH3 CH1 0.09805 0.0779 0.007638095 4.47E-03
functype[156]=LJ14, c6A= C CH2 0.04838 0.08642 0.004181 3.33E-03
functype[157]=LJ14, c6A= C C 0.04838 0.04838 0.002340624 2.34E-03
The values for N, C, O, H seems to be OK, but I have problems to get the
same value, when CH1, CH2, CH3 are involved. Since I do not have too much
experience, I would like to know how the value from the .tpr file can be
derived.

The other entry for LJ potential is the short range term LJ_SR (.tpr file

   ffparams:
      atnr=11
      ntypes=170
         functype[0]=LJ_SR, c6= 9.61380266e-03, c12= 2.66462448e-05
         functype[1]=LJ_SR, c6= 4.74365894e-03, c12= 1.14699596e-05
         functype[2]=LJ_SR, c6= 4.66325786e-03, c12= 5.16199998e-06

Unfortunately, I do not find the section where the function is assigned to
a specific pair of interaction. Where are these functions assigned to a
specific interaction? Furthermore, is it possible to distinguish between
intra-nonbonded (solute-solute) and inter-bonded (water-solute) interaction?

For you this might be an easy question to answer, and you immediately
realize there is a beginner at work, but nevertheless I would appreciate
any help.

All the best
Otto
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