Re: [gmx-users] REST simulation
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.fu...@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 Fuchspatrick.fuchs@univ-** paris-diderot.fr 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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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=CH3H0.09805000.00E+00 functype[155]=LJ14,c6A=CH3CH10.098050.0779 0.0076380954.47E-03 functype[156]=LJ14,c6A=CCH20.048380.08642 0.0041813.33E-03 functype[157]=LJ14,c6A=CC0.048380.04838 0.0023406242.34E-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
Re: [gmx-users] REST simulation
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. 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.fu...@univ-paris-diderot.fr mailto:patrick.fu...@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 Fuchspatrick.fuchs@univ-__paris-diderot.fr mailto: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
Re: [gmx-users] REST simulation
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.fu...@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/REMDhttp://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.frpatrick.fu...@univ-paris-diderot.fr mailto:patrick.fuchs@univ-**paris-diderot.frpatrick.fu...@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 Fuchspatrick.fuchs@univ-__**paris-diderot.frpatrick.fuchs@univ-__paris-diderot.fr mailto:patrick.fuchs@univ-**paris-diderot.frpatrick.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
Re: [gmx-users] REST simulation
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.fu...@univ-paris-diderot.fr mailto:patrick.fu...@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@univ-paris-__diderot.fr mailto:patrick.fu...@univ-paris-diderot.fr mailto:patrick.fuchs@univ-__paris-diderot.fr mailto:patrick.fu...@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 Fuchspatrick.fuchs@univ-paris-diderot.fr
Re: [gmx-users] REST simulation
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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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 0.0041813.33E-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= 5.1618e-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 listgmx-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
Re: [gmx-users] REST simulation
On 12/12/2011 8:42 PM, Patrick Fuchs 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. It's possible, but far from desirable to attempt to manipulate the contents of the .tpr directly. Instead, use grompp -pp to write a complete stand-alone topology, which you can then use as input to a script to do the appropriate solute parameter scaling for each replica. Then use grompp normally on the new set of .top files to generate a set of .tpr files that differ not only in lambda but in their solute parameters. Mark 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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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= 5.1618e-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] REST simulation
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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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=CH3H0.09805000.00E+00 functype[155]=LJ14,c6A=CH3CH10.098050.0779 0.0076380954.47E-03 functype[156]=LJ14,c6A=CCH20.048380.086420.004181 3.33E-03 functype[157]=LJ14,c6A=CC0.048380.048380.002340624 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= 5.1618e-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
Re: [gmx-users] REST simulation
Hi Mark, Thanks a lot. This was very helpful. I have also a question concerning single vs double precision gromacs simulation. Which one is more suitable for this kind of simulation and are there general rules to decide which precision should be used depending on the simulation? All the best Otto On 12 Dec 2011, at 12:55, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/12/2011 8:42 PM, Patrick Fuchs 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. It's possible, but far from desirable to attempt to manipulate the contents of the .tpr directly. Instead, use grompp -pp to write a complete stand-alone topology, which you can then use as input to a script to do the appropriate solute parameter scaling for each replica. Then use grompp normally on the new set of .top files to generate a set of .tpr files that differ not only in lambda but in their solute parameters. Mark 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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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= 5.1618e-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
Re: [gmx-users] REST simulation
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 Fuchspatrick.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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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=CH3H0.09805000.00E+00 functype[155]=LJ14,c6A=CH3CH10.098050.07790.007638095 4.47E-03 functype[156]=LJ14,c6A=CCH20.048380.086420.004181 3.33E-03 functype[157]=LJ14,c6A=CC0.048380.048380.002340624 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= 5.1618e-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
Re: [gmx-users] REST simulation
Hi Mark, good to know, this -pp option of grompp is very useful. Thanks! Ciao, Patrick Le 12/12/2011 12:55, Mark Abraham a écrit : On 12/12/2011 8:42 PM, Patrick Fuchs 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. It's possible, but far from desirable to attempt to manipulate the contents of the .tpr directly. Instead, use grompp -pp to write a complete stand-alone topology, which you can then use as input to a script to do the appropriate solute parameter scaling for each replica. Then use grompp normally on the new set of .top files to generate a set of .tpr files that differ not only in lambda but in their solute parameters. Mark 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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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= 5.1618e-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
[gmx-users] REST simulation
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.e+00, c12A= 0.e+00, c6B= 0.e+00, c12B= 0.e+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= 5.1618e-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 -- gmx-users mailing listgmx-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
