[gmx-users] REST simulation

[Mark Abraham]

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
>>
>>
>