[gmx-users] REST simulation
Otto Master
otto.master9 at gmail.com
Tue Dec 13 11:46:18 CET 2011
Hi Patrick,
thanks for your help. What I still do not understand is, how I can set-up
the replica simulation starting from the two equilibrated systems. What do
I have to put into the .mdp file and in the grompp command to consider the
two equilibrated configurations and further obtain the tpr files for the
different replica for different lambda values to interpolate between the
two configuration. I would be very glad if you could help me on that.
All the best
Otto
On Mon, Dec 12, 2011 at 1:50 PM, Patrick Fuchs <
patrick.fuchs at univ-paris-diderot.fr> wrote:
> Hi Otto,
> yes I copied those two files you mentionned (also .rtp for charges) in
> some specific directory to apply the appropriate scaling. But according to
> the authors this REST implementation, you just need that for the highest
> "temperature" (for the lowest, the Hamiltonian is unchanged) and then
> intermediate "temperatures" are interpolated using the lambda factor. So
> for equilibrating each replica, you just need to set the appropriate lambda
> value.
> Now I'd consider Mark's advice to use the -pp flag of grompp which might
> be convenient for scripting the scaling of the potential.
> Ciao,
>
> Patrick
>
> Le 12/12/2011 12:56, Otto Master a écrit :
>
> Hi Patrick,
>> Thanks a lot for your reply. Just to be sure, you create for every
>> replicate a copy of the original force field, and after you manipulate the
>> parameter in ffnonbonded.itp and ffbonded.itp. Then you go for each
>> replicate through the usual simulation preparation steps (minimisation,
>> nvt, equilibration ...). The result of this you use for the replicate
>> exchange simulation.
>>
>> Thanks a lot
>> Otto
>>
>> On 12 Dec 2011, at 10:42, Patrick Fuchs<patrick.fuchs at univ-**
>> paris-diderot.fr <patrick.fuchs at univ-paris-diderot.fr>> 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.
>>> 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<patrick.fuchs at univ-paris-diderot.fr>
>>> Web Site: http://www.dsimb.inserm.fr/~**fuchs<http://www.dsimb.inserm.fr/%7Efuchs>
>>> --
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>>
> --
> ______________________________**______________________________**
> ___________
> 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<patrick.fuchs at univ-paris-diderot.fr>
> Web Site: http://www.dsimb.inserm.fr/~**fuchs<http://www.dsimb.inserm.fr/%7Efuchs>
> --
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