[gmx-users] REST simulation

Mon Dec 12 12:56:04 CET 2011

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> 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
> Web Site: http://www.dsimb.inserm.fr/~fuchs
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