[gmx-users] REST simulation

[Patrick Fuchs]

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: patrick.fuchs at univ-paris-diderot.fr
Web Site: http://www.dsimb.inserm.fr/~fuchs