[gmx-users] REST simulation
Patrick Fuchs
patrick.fuchs at univ-paris-diderot.fr
Tue Dec 13 14:25:38 CET 2011
Hi Otto,
do you know how to use the free energy code in GROMACS for running
alchemical transformations (such as thermodynamic integration)? I
strongly suggest first to be confortable with that code before trying to
implement REST. In such alchemical calculations, you have to specify two
topologies, one for state A and one for state B. Then simulations at
each lambda value is a linear interpolation between state A and state B,
such as H = (1-lambda)*H[A] + lambda*H[B]. In the case of REST, one
simulation at an intermediate lambda value is also a linear
interpolation between topology A (ref T, unscaled Hamiltonian) and
topology B (highest T, scaled Hamiltonian). You thus have to build a
topology for both A *and* B (how to do that is well described in the
manual). Once you have this "dual" topology, you just have to set lambda
for each replica.
Ciao,
Patrick
Le 13/12/2011 14:05, Otto Master a écrit :
> 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
> <mailto: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
> <mailto:patrick.fuchs at univ-paris-diderot.fr>
> <mailto:patrick.fuchs at univ-__paris-diderot.fr
> <mailto: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
> <mailto:patrick.fuchs at univ-__paris-diderot.fr>
> <mailto:patrick.fuchs at univ-__paris-diderot.fr
> <mailto: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
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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>
> <tel:%2B33%20%280%291-44-49-__30-57> - Fax
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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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_______________________________________________________________________
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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