Re: [gmx-users] g_hbond
Dear David, Yes it is DGact. The DGeq follows from the fraction of COOH that are not forming hydrogen bonds, option -nhbdist. So, I need to use the equation (9) and (10) from your paper to calculate the equilibrium constant and free energy of H-bonding. Another question I have is, for a polycarboxylic acid system in water (COOH groups as side chains) for a 10ns run, I got the following as the output where the life time of the H-bond (between the polyacid and water) is negative. Is this correct? This means that the ACF has not equilibrated and you need much longer sims. You probably got a warning about it. I did not get a warning here. I also have simulations (20ns) of copolyacids where again it gave me negative life time. These runs are well equilibrated with respect to energy and Rg of the polymers. The system is a 20 repeat unit chain in approx. 5500 water molecules. I have done simulations in which 10 units are COO- and the remaining 10 as COOH along the chain. With a 10ns trajectory, the average life time of H-bonds is positive.Only in the case of unionized acid I am getting a negative life time. ACF 22057/22057 Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0146697 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward-0.271 -3.687-666.000 0.0146697 Backward -2.291 -0.437-666.000 One-way 0.101 9.882 10.207 Integral0.034 29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 What is the value for free energy of H-bonding. -- 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] g_hbond
On 2011-12-12 09:54, sulatha M. S wrote: Dear David, Yes it is DGact. The DGeq follows from the fraction of COOH that are not forming hydrogen bonds, option -nhbdist. So, I need to use the equation (9) and (10) from your paper to calculate the equilibrium constant and free energy of H-bonding. Yes. Another question I have is, for a polycarboxylic acid system in water (COOH groups as side chains) for a 10ns run, I got the following as the output where the life time of the H-bond (between the polyacid and water) is negative. Is this correct? This means that the ACF has not equilibrated and you need much longer sims. You probably got a warning about it. I did not get a warning here. I also have simulations (20ns) of copolyacids where again it gave me negative life time. These runs are well equilibrated with respect to energy and Rg of the polymers. The system is a 20 repeat unit chain in approx. 5500 water molecules. I have done simulations in which 10 units are COO- and the remaining 10 as COOH along the chain. With a 10ns trajectory, the average life time of H-bonds is positive.Only in the case of unionized acid I am getting a negative life time. Did you look at the ACF graph? It could be constant at 1 or 0. ACF 22057/22057 Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0146697 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward-0.271 -3.687-666.000 0.0146697 Backward -2.291 -0.437-666.000 One-way 0.101 9.882 10.207 Integral0.034 29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists What is the value for free energy of H-bonding. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Gromos parameters for atom type OA
Hi, slightly off-thread, I'd like to add that the oxygen parameters of 53a6 have been recently refined in a new set called 53a6OXY (http://pubs.acs.org/doi/abs/10.1021/ct1006407). So this ends up in new values for LJ and charges for the OA atom (as well as for other oxygen atoms). Cheers, Patrick Le 09/12/2011 20:03, Javier Cerezo a écrit : GROMOS force field builds the LJ parameters by multiplication of the square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12) labels). In the case of the repulsion term (C12), up to three of such parameters are possible: SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)), when combined with other atoms, depending on the desired repulsion strength (e.g. the enhanced C12(3) repulsion is used to keep charged groups separated). Which of the three is used depends on the combination of atoms, and is specified in an (asymmetric) matrix (see pages 14 and 15 in the pdf pages of 45a3 and 54a6 force fields from the GROMOS site, or in the ifp file the last lines for each atom type containing 1, 2 and 3). For the case of OA, this matrix specifies that the second C12 term is to be used when OA encountes another OA. So, according, to the ifp line you showed: C12(OA-OA) = SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 * 1.227E-3 = 1.50553E-6 Which is the same for 45a3 and 54a6 force fields. Differences in the parameters will show up only in the cases where the SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2)) Javier El 09/12/11 16:12, Samuli Ollila escribió: Dear all, I was comparing Gromos 45a3 and 53a6 force fields and I found something which I cannot understand. The atom type OA is described in ffG45a3nb.itp as: ;name at.num mass charge ptype c6 c12 OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 and in ffG53a6nb.itp: OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 which are same parameters. However, according to Gromos developers the atom type OA has been changed between Gromos 45a3 and 53a6. The parameters given by Gromos developers for 45a3 are # IAC TYPE SQRT(C6) SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)) 3 OA 0.04756 1.1250E-3 1.227E-3 0.0 and for 53a6 3 OA 0.04756 1.100E-3 1.227E-3 0.0 The actual numbers are different for parameters used in Gromacs since the way to write parameters is different. My problem is that there is difference in OA type between 45a3 and 53a6 in parameters given by Gromos developers but not in the files distributed in Gromacs package. Can someone explain this? BR, Samuli Ollila -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- ___ 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
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
Re: [gmx-users] Information about g_sas
Alex Jemulin wrote: Dear all Which is the difference between hydropilic and hydrophobic sas? g_sas computes hydrophobic and hydrophilic surface area based on the absolute value of the partial charge of the atom, which can be adjusted with the -qmax flag. How can give an interpretation to g_sas xvg graph? Interpretation of the results is based on the question being asked and the group being analyzed, things that only you know. What can I find out in it and how can use g_sas to analyze a trajectory? Start by reading g_sas -h. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] g_hbond
I did not get a warning here. I also have simulations (20ns) of copolyacids where again it gave me negative life time. These runs are well equilibrated with respect to energy and Rg of the polymers. The system is a 20 repeat unit chain in approx. 5500 water molecules. I have done simulations in which 10 units are COO- and the remaining 10 as COOH along the chain. With a 10ns trajectory, the average life time of H-bonds is positive.Only in the case of unionized acid I am getting a negative life time. Did you look at the ACF graph? It could be constant at 1 or 0. Yes, the ACF decays to 0 and remains constant in all cases Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists What is the value for free energy of H-bonding. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- 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
[gmx-users] error while adding charges to the system using genion
Dear all, i need to add 8 positive ions to my system..its a membrane protein enveloped inside a solvent box..when i am running the genion command for addition of 8 positive ions to the system, its showing an error your solvent group size (6173) is not a multiple of 11...what does this mean...??... how can i rectify this error??...plz help Thanks.. -- *Nishith Saurav Topno Research Scholar Centre for Bioinformatics Pondicherry University Puducherry-605014 * -- 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
[gmx-users] Force field for polymer molecule - tips
Hi. I would like to use a CHARMM (CGennFF based) of polymer molecule in Gromacs. The polymer is composed of three different monomer and two different terminal residues (one for each of the the two terminals) - five residues in total. The CHARMM generalized FF has already been ported to Gromacs so judging from the documentation (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) I should create a monomeres.rtp (arbitrary name?) file containing the information about the monomeres. Any tips on doing that? The general workflow will be: Generate the initial structure of the polymer of a given composition using Charmm* and save the coordinates as a PDB (plus two other files). Then supply the generated PDB to pdb2gmx to generate the initial GRO file. Second question: How will pdb2gmx know it has to parse the monomeres.rtp file? * - so far the only package that can generate the initial structures from a set of internal coordinates in the force field. Thanks in advance, Jernej Zidar -- 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] error while adding charges to the system using genion
On 13/12/2011 4:55 PM, Nishith Saurav Topno wrote: Dear all, i need to add 8 positive ions to my system..its a membrane protein enveloped inside a solvent box..when i am running the genion command for addition of 8 positive ions to the system, its showing an error your solvent group size (6173) is not a multiple of 11...what does this mean...??... how can i rectify this error??...plz help genion has to remove solvent molecules (IIRC named SOL) from your system, but the contents of your [molecules] directive and/or coordinate file don't make sense to genion. Mark -- 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] Force field for polymer molecule - tips
On 13/12/2011 5:06 PM, Jernej Zidar wrote: Hi. I would like to use a CHARMM (CGennFF based) of polymer molecule in Gromacs. The polymer is composed of three different monomer and two different terminal residues (one for each of the the two terminals) - five residues in total. The CHARMM generalized FF has already been ported to Gromacs so judging from the documentation (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) I should create a monomeres.rtp (arbitrary name?) file containing the information about the monomeres. Any tips on doing that? The general workflow will be: Generate the initial structure of the polymer of a given composition using Charmm* and save the coordinates as a PDB (plus two other files). Then supply the generated PDB to pdb2gmx to generate the initial GRO file. Second question: How will pdb2gmx know it has to parse the monomeres.rtp file? It can't. You must add to an existing .rtp file. Mark -- 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
[gmx-users] Coupling groups for nvt equilibration
Dear Gromacs users, I am simulating a system containing a protein with covalently attached Mg in complex with GDP. For nvt equilibration, I have taken protein+Mg+GDP as the single group and Water+ions as the other. The corresponding block from the .mdp file is below: -- ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein_MG_GDP Water_and_ions Is this coupling method correct, to treat Protein and Mg as different quantities? Thanks --- Neeru Sharma Pune (India) -- 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
[gmx-users] g_rms on large amount of data
Hi, I'm using Gromacs 4.5.5 to simulate a protein in explicit solvent. The simulation is running fine and I have collected 9 100ns simulations. I'm eliminating the first 50 ns for equilibration and sheer data size. What I want to do now is to cluster the simulations based on rmsd of certain residues. I have used make_ndx to select the residues and made a group. I have used trjcat -cat option to concatenate the 9 runs into a single giant .xtc file. In the .xtc file, I only output the protein. My plan was to use g_rms to create a rmsd.xpm table and using that with g_cluster. However, when I do run g_rms, it seems like it will take weeks to finish. The RMSD matrix size becomes 225000x225000 and my question is: How do you cluster this much data? Any recommendation would be useful. Thank you for your time. -- 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
