[gmx-users] REST simulation
Otto Master
otto.master9 at gmail.com
Tue Dec 13 14:05:22 CET 2011
Hi Patrick,
again thanks a lot for your valuable help. But I do not get my head around
how to tell grompp that for lambda=0 I would like to use the the unscaled
Hamiltonian and for lambda=1 the highest "temperature". In the tutorial the
change in temperature is a number which is passed to the pre-processor, but
for REST a number (lambda=0 and lambda=1) corresponds to different
topology, which are written in a file. I do not know how to specify that.
What is the identifier or should I pass something additionally to grompp,
referring to the two topology files?
Ciao,
Otto
On Tue, Dec 13, 2011 at 1:23 PM, Patrick Fuchs <
patrick.fuchs at univ-paris-diderot.fr> wrote:
> Hi Otto,
> you have to equilibrate at each lambda value! The unscaled Hamiltionian is
> your lowest "temperature", say 300K, which corresponds to lambda=0. You
> generate the highest "temperature" by appropriately scaling the
> Hamiltonian, say 600K, which corresponds to lambda=1. Then you create n
> directories, one for each replica. In each directory, you set a different
> lambda value from 0 to 1 in the mdp file and you equilibrate each replica.
> At the end, you obtain n gro files that can serve as input to generate n
> tpr files for the REMD run.
> I think this is the standard flow for REMD as explained in:
> http://www.gromacs.org/**Documentation/How-tos/REMD<http://www.gromacs.org/Documentation/How-tos/REMD>.
> The only difference is that you use a different lambda value, so a
> different Hamiltonian, instead of a different temperature for each replica.
> Ciao,
>
> Patrick
>
> Le 13/12/2011 11:46, Otto Master a écrit :
>
>> 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<patrick.fuchs at univ-paris-diderot.fr>
>> <mailto:patrick.fuchs at univ-**paris-diderot.fr<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>
>> <mailto: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
>> <tel:%2B33%20%280%291-44-49-**30-57> - Fax : +33
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>> >
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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 <tel:%2B33%20%280%291-44-49-**30-57> - Fax
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>> <mailto:patrick.fuchs at univ-**paris-diderot.fr<patrick.fuchs at univ-paris-diderot.fr>
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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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