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.fu...@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 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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-requ...@gromacs.org. Can't post? Read 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.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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-requ...@gromacs.org.
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