[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
>>            (0)1-43-06-50-19 <tel:%2B33%20%280%291-43-06-**50-19>
>>            E-mail address: 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>
>> >
>>            Web Site: http://www.dsimb.inserm.fr/~__**fuchs<http://www.dsimb.inserm.fr/%7E__fuchs>
>>            <http://www.dsimb.inserm.fr/%**7Efuchs<http://www.dsimb.inserm.fr/%7Efuchs>
>> >
>>
>>            --
>>            gmx-users mailing list gmx-users at gromacs.org
>>            <mailto:gmx-users at gromacs.org>
>>            http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>>
>>            <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>>            Please search the archive at
>>            http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>>
>>            <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>
>> before
>>            posting!
>>            Please don't post (un)subscribe requests to the list. Use
>>            the www interface or send it to
>>            gmx-users-request at gromacs.org
>>            <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>            Can't post? Read
>>            http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>>            <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>    --
>>    ______________________________**______________________________**
>> _______________
>>
>>    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 (0)1-43-06-50-19 <tel:%2B33%20%280%291-43-06-**50-19>
>>    E-mail address: 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>
>> >
>>    Web Site: http://www.dsimb.inserm.fr/~__**fuchs<http://www.dsimb.inserm.fr/%7E__fuchs>
>>    <http://www.dsimb.inserm.fr/%**7Efuchs<http://www.dsimb.inserm.fr/%7Efuchs>
>> >
>>
>>    --
>>    gmx-users mailing list gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>>
>>    <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>>    Please search the archive at
>>    http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>>
>>    <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>
>> before posting!
>>    Please don't post (un)subscribe requests to the list. Use the www
>>    interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>    Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>>    <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>
>>
>>
> --
> ______________________________**______________________________**
> ___________
> 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>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111213/2bbe89c2/attachment.html>


More information about the gromacs.org_gmx-users mailing list