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 < [email protected]> 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@univ-paris-**diderot.fr<[email protected]> >> <mailto:patrick.fuchs@univ-**paris-diderot.fr<[email protected]>>> >> 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@univ-__**paris-diderot.fr<patrick.fuchs@univ-__paris-diderot.fr> >> >> <mailto:patrick.fuchs@univ-**paris-diderot.fr<[email protected]>>> >> 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@univ-paris-__**diderot.fr<patrick.fuchs@univ-paris-__diderot.fr> >> >> <mailto:patrick.fuchs@univ-**paris-diderot.fr<[email protected]> >> > >> 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 [email protected] >> <mailto:[email protected]> >> >> 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 >> [email protected] >> >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> 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@univ-paris-__**diderot.fr<patrick.fuchs@univ-paris-__diderot.fr> >> >> <mailto:patrick.fuchs@univ-**paris-diderot.fr<[email protected]> >> > >> 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 [email protected] >> <mailto:[email protected]> >> >> 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. 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