Hi Mark,
good to know, this -pp option of grompp is very useful. Thanks!
Ciao,
Patrick
Le 12/12/2011 12:55, Mark Abraham a écrit :
On 12/12/2011 8:42 PM, Patrick Fuchs wrote:
Hi Otto,
in my lab we tried to implement this REST variant in GROMACS as
proposed by those authors. We figured out that it was easier to
manipulate directly the parameters files in the top directory. There
you know exactly what you are doing; recall that some interactions
(i.e. solvent/solvent) mustn't be scaled whereas some others have to
be scaled (solute/solute and solute/solvent).
It's probably possible to do it in the tpr file, but it looked less
trivial to me: i) you have to know how atoms are coded in the file
(e.g. in the functype[???]=LJ_SR[...] matrix, you have to understand
how atom numbers are coded there), ii) you have to regenerate a tpr
from plain text file; it's probably doable, but I don't know how.
Actually, maybe some developers can tell if it's possible.
It's possible, but far from desirable to attempt to manipulate the
contents of the .tpr directly.
Instead, use grompp -pp to write a complete stand-alone topology, which
you can then use as input to a script to do the appropriate solute
parameter scaling for each replica. Then use grompp normally on the new
set of .top files to generate a set of .tpr files that differ not only
in lambda but in their solute parameters.
Mark
Good luck,
Patrick
Le 08/12/2011 19:01, Otto Master a écrit :
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
--
_______________________________________________________________________
Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19
E-mail address: [email protected]
Web Site: http://www.dsimb.inserm.fr/~fuchs
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