Re: [gmx-users] Re: PRODRG tools
Hi all, For the GROMOS force field there's also the automated topology builder (ATB) from Alpesh Malde and Alan Mark: http://compbio.biosci.uq.edu.au/atb/ Cheers, René = René Pool Division of Molecular and Computational Toxicology Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV AMSTERDAM, the Netherlands - IBIVU/Bioinformatics Department of Computer Science Vrije Universiteit Amsterdam De Boelelaan 1081a 1081HV AMSTERDAM, the Netherlands Room P 2.75 E: r.p...@vu.nl T: +31 20 598 76 12 F: +31 20 598 76 10 = On 07/31/2011 05:21 PM, Andrej Frolov wrote: Hello, There are several ways to get the topology + force field for an arbitrary molecule: 1. Maestro + Desmond programs of the Schrodinger software pack can assign OPLS-AA force filed. The parameters are stored in the *.cms file. 2. FFLD_SERVER of the Schrodinger software: $SCHRODINGER/utilities/ffld_server. Also OPLS-AA force filed. You will need to write a script which converts the output to Gromacs format. 3. antechamber + tleap of the AmberTools utilities. It can assign any kind of Amber force field, like General Amber Force Field. See an example:http://compchemmpi.wikispaces.com/Scripts#GenAmberTop You could use the amb2gmx script to convert the generated Amber topology to Gromacs format: http://ffamber.cnsm.csulb.edu/ffamber-tools.html 4. ''PRODRG server'' for the united atom GMX force fields. 5. ''Vega ZZ'' and Vega can assign OPLS-AA force field, but not all atom types, bonds etc. are supported. 6. MCCCS Towhee'' monte carlo code can assign very many force fields, but, first, one has to create the so-called basic connectivity map (which atom is covalently bound to which). http://towhee.sourceforge.net/ Kind regards, Andrey -- Andrey Frolov PhD student Max Planck Institute for Mathematics in the Sciences (MPI f. Mathematik in den Naturwissenschaften) Inselstr. 22-26, 04103 Leipzig, Germany e-mail: fro...@mis.mpg.de web: http://www.mis.mpg.de/scicomp/CompPhysChem/GroupMain.html Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. Best Shiyong -- 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] large error bars in PMF
Hello, some days ago you had recomended me to use a dodecahedron box and pull_dim = Y Y Y to try to decrease some error bars I was obtaining in my PMF calculations (trying to calculate the binding energy of two cyclic peptides). Now, I have run these calaculations, but I have a doubt for the analysis. How should I analyze the results, using g_wham like in the case of pull_dim = N N Y. I have not seen any option in g_wham to indicate this is a 3D PMF. I have also seen in this list these days that 3D-Wham was recomended (for a case different to mine). So, how should analyze the results obtaind from pull_dim = Y Y Y ? Thanks a lot for your help. Best wishes, Rebeca. From: rega...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] large error bars in PMF Date: Fri, 22 Jul 2011 12:41:34 + I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total pulling was 5nm along the z direction. I dont´t think there could be a problem with the PBC, since the layer of solvent around the protein is quite big, although I suppose that using a dodecahedron box for this system would have been better. I will try now the pull_dim = Y Y Y and see what it happens. Thanks a lot for the suggestions! Best wishes, Rebeca. Date: Fri, 22 Jul 2011 08:23:18 -0400 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] large error bars in PMF I see now what you mean. As it happens, I doubt that this would have caused the problem since no force was applied on X and Y dimensions, so it would require that there was a PBC-based distance degeneracy along Z, although this is of course possible and hopefully Rebecca will answer this part. Also, thanks for the pull_dimension/pull_vec fix. Chris. -- original message -- chris.ne...@utoronto.ca wrote: [Hide Quoted Text] I don't see why the box-type makes any difference whatsoever. It is possible that if you use a rhombic dodecahedron, you may reduce the system size, thus simulate more ns/day, thus converge faster, but that should be the only effect. I would be interested to hear more from Justin about how the box-shape is expected to affect peptide rotation... perhaps I misunderstand this point. My point was not that the box shape has any effect on protein rotation. That will happen regardless of the box shape, of course. My suggestion for this box type was that since Rebeca has a system that is essentially spherically symmetric (i.e. two proteins connected by some arbitrary vector, which are at the same time rotating freely), then she must use a suitable box shape that reflects this type of symmetry. I never got a clear answer to whether or not the weird interactions she cited were due to PBC or not, but if one uses a rectangular box for a system like this one, there can be artificial interactions very easily. [Hide Quoted Text] I have a few other comments. 1. If you allow the peptide to rotate freely, then you do indeed need to converge all of their different rotational interactions. An alternative is to apply orientational restraints during the pulling (assuming that you know the bound state) and then to correct to an unrestrained state at large separations. You can see, for instance, D. L. Mobley, J. D. Chodera, K. A. Dill. On the use of orientational restraints and symmetry number corrections in alchemical free energy calculations, ... 2. You are using pull_dim = N N Y which, if I haven't entirely forgotten how the pull-code works, means that the distance along Z is restrained but the distance along X and Y is free to change. What you end up with by sampling in this way is pretty strange and will require a really weird volumetric correction in the absence of infinite sampling time. You must decide to either: (i) pull to a spherical distance: pull_dim = Y Y Y pull_geometry = distance or (ii) to pull along a defined vector pull_dim = Y Y Y pull_geometry = direction Just a note here - if you set direction geometry, the pull_dim keyword is not used, but pull_vec is. -Justin [Hide Quoted Text] What you have done: pull_dim = N N Y pull_geometry = distance is only really useful when the system is isotropic along the XY plane (at least in the time averaged sense), such as for a lipid bilayer, or when the freedom in X and Y is very low, such as in a channel. 3. Finally, just because you sampled *more* doesn't mean that your values are converged. Look into block averaging and test to see if your binding free energy is drifting over time. Good luck, Chris. -- original message -- Hi again, I have one doub about the suggestion of using a dodecahedral box for my umbrella sampling to remove the problems I am having with the peptides rotating. I cannot see why a dodecaheral box is going to avoid this. Would it be better a truncated octahedron? Thanks a lot for your help. Best wishes, Rebeca. ... snip... --
Re: [gmx-users] large error bars in PMF
Rebeca García Fandiño wrote: Hello, some days ago you had recomended me to use a dodecahedron box and pull_dim = Y Y Y to try to decrease some error bars I was obtaining in my PMF calculations (trying to calculate the binding energy of two cyclic peptides). Now, I have run these calaculations, but I have a doubt for the analysis. How should I analyze the results, using g_wham like in the case of pull_dim = N N Y. I have not seen any option in g_wham to indicate this is a 3D PMF. I have also seen in this list these days that 3D-Wham was recomended (for a case different to mine). So, how should analyze the results obtaind from pull_dim = Y Y Y ? Just as you would previously. -Justin Thanks a lot for your help. Best wishes, Rebeca. From: rega...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] large error bars in PMF Date: Fri, 22 Jul 2011 12:41:34 + I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total pulling was 5nm along the z direction. I dont´t think there could be a problem with the PBC, since the layer of solvent around the protein is quite big, although I suppose that using a dodecahedron box for this system would have been better. I will try now the pull_dim = Y Y Y and see what it happens. Thanks a lot for the suggestions! Best wishes, Rebeca. Date: Fri, 22 Jul 2011 08:23:18 -0400 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] large error bars in PMF I see now what you mean. As it happens, I doubt that this would have caused the problem since no force was applied on X and Y dimensions, so it would require that there was a PBC-based distance degeneracy along Z, although this is of course possible and hopefully Rebecca will answer this part. Also, thanks for the pull_dimension/pull_vec fix. Chris. -- original message -- chris.ne...@utoronto.ca wrote: [Hide Quoted Text] I don't see why the box-type makes any difference whatsoever. It is possible that if you use a rhombic dodecahedron, you may reduce the system size, thus simulate more ns/day, thus converge faster, but that should be the only effect. I would be interested to hear more from Justin about how the box-shape is expected to affect peptide rotation... perhaps I misunderstand this point. My point was not that the box shape has any effect on protein rotation. That will happen regardless of the box shape, of course. My suggestion for this box type was that since Rebeca has a system that is essentially spherically symmetric (i.e. two proteins connected by some arbitrary vector, which are at the same time rotating freely), then she must use a suitable box shape that reflects this type of symmetry. I never got a clear answer to whether or not the weird interactions she cited were due to PBC or not, but if one uses a rectangular box for a system like this one, there can be artificial interactions very easily. [Hide Quoted Text] I have a few other comments. 1. If you allow the peptide to rotate freely, then you do indeed need to converge all of their different rotational interactions. An alternative is to apply orientational restraints during the pulling (assuming that you know the bound state) and then to correct to an unrestrained state at large separations. You can see, for instance, D. L. Mobley, J. D. Chodera, K. A. Dill. On the use of orientational restraints and symmetry number corrections in alchemical free energy calculations, ... 2. You are using pull_dim = N N Y which, if I haven't entirely forgotten how the pull-code works, means that the distance along Z is restrained but the distance along X and Y is free to change. What you end up with by sampling in this way is pretty strange and will require a really weird volumetric correction in the absence of infinite sampling time. You must decide to either: (i) pull to a spherical distance: pull_dim = Y Y Y pull_geometry = distance or (ii) to pull along a defined vector pull_dim = Y Y Y pull_geometry = direction Just a note here - if you set direction geometry, the pull_dim keyword is not used, but pull_vec is. -Justin [Hide Quoted Text] What you have done: pull_dim = N N Y pull_geometry = distance is only really useful when the system is isotropic along the XY plane (at least in the time averaged sense), such as for a lipid bilayer, or when the freedom in X and Y is very low, such as in a channel. 3. Finally, just because you sampled *more* doesn't mean that your values are converged. Look into block averaging and test to see if your binding free energy is drifting over time. Good luck, Chris. -- original message -- Hi again, I have one doub about the suggestion of using a dodecahedral box for my umbrella sampling to remove the problems I am
[gmx-users] atom types
Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you say that nonbonded pair interactions are not Coulombic. Surely nonbonded charged atoms interact with each other, when close enough? (or by Nonbonded pair interactions do you explcitly mean 1-4,1-5, etc.) What are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Gavin Melaugh wrote: Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you say that nonbonded pair interactions are not Coulombic. Surely nonbonded charged atoms interact with each other, when close enough? (or by Nonbonded pair interactions do you explcitly mean 1-4,1-5, etc.) What are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the purpose of [pairtype] generation is for LJ terms only. They are special 1-4 interactions between different atomtypes. Look at any force field for which [pairtypes] are listed - they have only C6 and C12 terms. Charges are not used for these calculations, but they are applied later during the MD using normal Coulombic equations and FudgeQQ. -Justin Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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
[gmx-users] g_disre problems
Hello Everyone! I'm with problems using g_disre where, after de execution, the answer is always Segmentation fault. To minimize the problem I changed for a very small system in the tutorial sub-directory of gromacs VERSION 4.5.4. I'm not using mpi library. The distance restraints are: [ distance_restraints ] ; aiaj typeindex typelow up1 up2 fac 15 53 1 0 1 0.0 0.3 0.4 1.0 15 54 1 0 1 0.0 0.3 0.4 1.0 15 55 1 0 1 0.0 0.3 0.4 1.0 17 53 1 0 1 0.0 0.3 0.4 1.0 17 54 1 0 1 0.0 0.3 0.4 1.0 17 55 1 0 1 0.0 0.3 0.4 1.0 15 38 1 1 1 0.0 0.3 0.4 1.0 15 39 1 1 1 0.0 0.3 0.4 1.0 17 38 1 1 1 0.0 0.3 0.4 1.0 17 39 1 1 1 0.0 0.3 0.4 1.0 To analyse: g_disre -s topol.tpr -f traj.trr and the answer is: Back Off! I just backed up disres.log to ./#disres.log.2# Reading file ../topol.tpr, VERSION 4.5.4 (single precision) Reading file ../topol.tpr, VERSION 4.5.4 (single precision) Segmentation fault (core dumped) in the file /var/log/messages Aug 1 15:19:03 camboinhas kernel: g_disre[5743]: segfault at 4 ip 7f71869e4222 sp 7fff2970e170 error 4 in libgmx.so.6.0.0[7f7186987000+3b8000] Aug 1 15:19:03 camboinhas abrt[5744]: saved core dump of pid 5743 (/usr/local/gromacs/bin/g_disre) to /var/spool/abrt/ccpp-131743-5743.new/coredump (622592 bytes) This results are the same in my MDs I tried to recompile but the result is the same. Looking forward for your kind suggestions and comments Great Thanks Francisco -- Francisco Gomes Neto Laboratório de RMN de biomoléculas (bioNMR) Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Av. Carlos Chagas Filho, 373, CCS, Bloco K, Anexo CNRMN Rio de Janeiro, RJ, 21941-902 Phone: +55-21-3717-2019/3521-5558 Fax: +55-21-3881-4155 mobile:+55-21-9937-1621 fgo...@cnrmn.bioqmed.ufrj.br http://cnrmn.bioqmed.ufrj.br -- 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_disre problems
Francisco Gomes Neto wrote: Hello Everyone! I'm with problems using g_disre where, after de execution, the answer is always Segmentation fault. To minimize the problem I changed for a very small system in the tutorial sub-directory of gromacs VERSION 4.5.4. I'm not using mpi library. The distance restraints are: [ distance_restraints ] ; aiaj typeindex typelow up1 up2 fac 15 53 1 0 1 0.0 0.3 0.4 1.0 15 54 1 0 1 0.0 0.3 0.4 1.0 15 55 1 0 1 0.0 0.3 0.4 1.0 17 53 1 0 1 0.0 0.3 0.4 1.0 17 54 1 0 1 0.0 0.3 0.4 1.0 17 55 1 0 1 0.0 0.3 0.4 1.0 15 38 1 1 1 0.0 0.3 0.4 1.0 15 39 1 1 1 0.0 0.3 0.4 1.0 17 38 1 1 1 0.0 0.3 0.4 1.0 17 39 1 1 1 0.0 0.3 0.4 1.0 To analyse: g_disre -s topol.tpr -f traj.trr and the answer is: Back Off! I just backed up disres.log to ./#disres.log.2# Reading file ../topol.tpr, VERSION 4.5.4 (single precision) Reading file ../topol.tpr, VERSION 4.5.4 (single precision) Segmentation fault (core dumped) in the file /var/log/messages Aug 1 15:19:03 camboinhas kernel: g_disre[5743]: segfault at 4 ip 7f71869e4222 sp 7fff2970e170 error 4 in libgmx.so.6.0.0[7f7186987000+3b8000] Aug 1 15:19:03 camboinhas abrt[5744]: saved core dump of pid 5743 (/usr/local/gromacs/bin/g_disre) to /var/spool/abrt/ccpp-131743-5743.new/coredump (622592 bytes) This results are the same in my MDs I tried to recompile but the result is the same. Looking forward for your kind suggestions and comments This is a known bug in g_disre: http://redmine.gromacs.org/issues/766 There is no fix yet. -Justin Great Thanks Francisco -- Francisco Gomes Neto Laboratório de RMN de biomoléculas (bioNMR) Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Av. Carlos Chagas Filho, 373, CCS, Bloco K, Anexo CNRMN Rio de Janeiro, RJ, 21941-902 Phone: +55-21-3717-2019/3521-5558 Fax: +55-21-3881-4155 mobile:+55-21-9937-1621 fgo...@cnrmn.bioqmed.ufrj.br http://cnrmn.bioqmed.ufrj.br -- 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
[gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water
Hi, I am sorry to bring up a several-days-old post, but if you have time, I am wondering if you can please help me with two concepts related to the pdf file at http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf and Justin's comments on it. 1. For temperature coupling in NVT simulations, what is a reasonable value for the time constant for coupling (tau_t)? In my previous simulation in which I used tcoupl = v-rescale, I chose tau_t = 2.0 ps. Justin kindly suggested that this may be a bit long for V-rescale. Would a value of, for example, tau_t = 1.0 ps be more reasonable, or should I use something even shorter? 2. How do you determine, as a rule of thumb, what to use for vdw cutoffs? For other simulations of water (i.e., another configuration), I had been using cutoffs such as rlist = rvdw = 1.0 nm, and I had been getting good results. However, a few weeks ago, I switched to a new, more interesting configuration, and I have been having some trouble with it, as described in my previous posts in this thread. Someone (not on this mailing list) suggested that I increase the vdw cutoffs in case the long-range vdw interactions would make a significant difference. So, in my last simulation, for example, I used rlist = rvdw = 2.3 nm. I chose this because my simulation box is a cube of edgelength 4.71 nm, and the cutoffs must be less than half the largest box length in order to obey the minimum image convention. Is it always (or usually) OK to use as large of cutoffs as possible without violating the minimum image convention? Of course, by making cutoffs longer than necessary, I am taking a huge hit in terms of performance. But performance aside, is there ever any danger (in terms of accuracy) of making the cutoffs too long? I wouldn't think so, but I am not sure. Or, does making the cutoffs too long lead to the flying ice cube problem? Looking at the article here: http://en.wikipedia.org/wiki/Flying_ice_cube, it seems that the flying ice cube problem is more likely related to the choice of temperature coupling (it seems my choice of V-rescale was poor; in my next simulation perhaps I should try Nose-Hoover) and possibly intergration algorithm, rather than related to cutoff lengths. Do you think that this is a correct interpretation? Thank you very much. Andrew DeYoung Carnegie Mellon University Andrew DeYoung wrote: Hi, Thank you. I tried again, this time doing 100 ps of NVT equlibration, followed by 500 ps of NVE. I have posted my results here: http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf But, they are not much better. For the NVT equilibration, I used v-rescale temperature coupling with tau_t = 2 ps. What kind of temperature coupling do you typically use or recommend? That sounds reasonable, although a 2-ps coupling time is a bit long for V-rescale. Your results indicate that the system still is not stable, even in NVT. Temperature should not fluctuate very much after the first few ps. Try a longer NVT. What motivated your choice of cutoffs? They seem arbitrary and too long. You may be seeing effects of the classic flying ice cube problem where isolated elements of the system start to (essentially) freeze. -Justin Thanks, Andrew Andrew DeYoung wrote: Hi, I have been simulating 1000 SPC/E water molecules in the NVE ensemble (by using tcoupl = no and pcoupl = no). In these simulations, I am considering only Lennard-Jones interactions; I have turned charges off by setting the partial charges on oxygen and hydrogen to zero in a local copy of spce.itp that I include in my topology file. If you have time, I have posted a pdf file containing a summary of what I have tried so far: http://www.andrew.cmu.edu/user/adeyoung/july27/july27.pdf At first, I tried using vdwtype = Cut-off. However, Gromacs gave me a note message: --- NOTE: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) --- I ignored this note message and ran the simulation anyway. Indeed, as Gromacs warned me, the (total) energy conservation is very bad; the total energy decreases seemingly significantly in what appears to be an almost linear fashion. I have done energy minimization, equilibration, and production dynamics, but for simplicity, I have drawn the equilibration and production dynamics results in the same color in the pdf file that I have posted. (As far as energy minimization, I did a series of two energy minimization steps. First, I used integrator = l-bfgs with dt = 0.001 ps, nsteps = 1, emstep = 0.01 nm, and emtol = 10.0 kJ mol^-1 nm^-1. I got the following results: Low-Memory BFGS Minimizer converged to Fmax 10 in 0 steps Potential Energy = -9.3022546e+02 Maximum force = 5.5933684e-01 on atom 1123 Norm of force = 1.9135195e-01 So, it seems that the energy of the configuration is quite low--the water molecules
[gmx-users] dispersion corrections in an anisotropic system
Dear GROMACS users,my system is composed of a repulsive surface with chains grafted on it and other free chains above this immobilized system. I am hesitating whether to use dispersion corrections for the pressure and energy or not. Without these corrections the repulsion of the grafting surface increases which is understandable. This is however, no a problem because under such conditions I can decrease this repulsion by the manipulation of LJ parameters. However, I think that the dispersion corrections are necessary for representation of the interactions between the bulk free chains wetting the anchored chains. Though in the melt they should be screened, but I am varying the densities of the system and not all cases represent melt situation. I have checked the mailing list but I have not found satisfactory answer. I have not found some way how to treat long range interactions of heterogeneous system.My next question is very trivial, but I can not find in Manual and other sources meaning of AllEnerPres.Thank you for your answer in advance.GreetingsZuzana -- 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] dispersion corrections in an anisotropic system
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[gmx-users] umbrella sampling using replica exchange
Hi, I was wondering whether in gromacs 4, one can use replica exchange simulation in combination with umbrella sampling. Thanks Sanku-- 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] Re: Improving Energy Conservation in NVE Simulation of Water
Andrew DeYoung wrote: Hi, I am sorry to bring up a several-days-old post, but if you have time, I am wondering if you can please help me with two concepts related to the pdf file at http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf and Justin's comments on it. 1. For temperature coupling in NVT simulations, what is a reasonable value for the time constant for coupling (tau_t)? In my previous simulation in which I used tcoupl = v-rescale, I chose tau_t = 2.0 ps. Justin kindly suggested that this may be a bit long for V-rescale. Would a value of, for example, tau_t = 1.0 ps be more reasonable, or should I use something even shorter? The minimum for tau_t is a magnitude 10x your timestep. Values of tau_t are often as low as 0.1 - 0.5 ps. It is easy to test if this improves your results. Pressure coupling, however, is different and generally these values would be too small. For temperature coupling with weak coupling methods, though, there shouldn't be a problem. Coupling too tightly can result in fixed kinetic energy which is unreasonable, so don't set tau_t = dt :) 2. How do you determine, as a rule of thumb, what to use for vdw cutoffs? For other simulations of water (i.e., another configuration), I had been using cutoffs such as rlist = rvdw = 1.0 nm, and I had been getting good results. However, a few weeks ago, I switched to a new, more interesting configuration, and I have been having some trouble with it, as described in my previous posts in this thread. Someone (not on this mailing list) suggested that I increase the vdw cutoffs in case the long-range vdw interactions would make a significant difference. So, in my last simulation, for example, I used rlist = rvdw = 2.3 nm. I chose this because my simulation box is a cube of edgelength 4.71 nm, and the cutoffs must be less than half the largest box length in order to obey the minimum image convention. Is it always (or usually) OK to use as large of cutoffs as possible without violating the minimum image convention? Of course, by making cutoffs longer than necessary, I am taking a huge hit in terms of performance. But performance aside, is there ever any danger (in terms of accuracy) of making the cutoffs too long? I wouldn't think so, but I am not sure. Force field models are parameterized to work under a given set of circumstances that include cutoffs and other parameters. Arbitrarily increasing cutoffs can absolutely induce artifacts, and I would say it is far more likely that such changes cause problems rather than preventing them. A few relevant posts to consider: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047586.html http://lists.gromacs.org/pipermail/gmx-users/2009-December/047593.html Refer to the primary literature for whatever parameters you're using. Rule of thumb: unless you can demonstrate that your conditions better represent reality (or are at least similarly accurate), don't mess with them. Or, does making the cutoffs too long lead to the flying ice cube problem? Looking at the article here: http://en.wikipedia.org/wiki/Flying_ice_cube, it seems that the flying ice cube problem is more likely related to the choice of temperature coupling (it seems my choice of V-rescale was poor; in my next simulation perhaps I should try Nose-Hoover) and possibly intergration algorithm, rather than related to cutoff lengths. Do you think that this is a correct interpretation? My mistake. In my head I equated the flying ice cube with the artificial ordering and density increases that can happen from arbitrary increases to cutoff values. There is a relationship between cutoffs, thermostats, and equipartition of energy, but it's not immediately relevant here. -Justin Thank you very much. Andrew DeYoung Carnegie Mellon University Andrew DeYoung wrote: Hi, Thank you. I tried again, this time doing 100 ps of NVT equlibration, followed by 500 ps of NVE. I have posted my results here: http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf But, they are not much better. For the NVT equilibration, I used v-rescale temperature coupling with tau_t = 2 ps. What kind of temperature coupling do you typically use or recommend? That sounds reasonable, although a 2-ps coupling time is a bit long for V-rescale. Your results indicate that the system still is not stable, even in NVT. Temperature should not fluctuate very much after the first few ps. Try a longer NVT. What motivated your choice of cutoffs? They seem arbitrary and too long. You may be seeing effects of the classic flying ice cube problem where isolated elements of the system start to (essentially) freeze. -Justin Thanks, Andrew Andrew DeYoung wrote: Hi, I have been simulating 1000 SPC/E water molecules in the NVE ensemble (by using tcoupl = no and pcoupl = no). In these simulations, I am considering only Lennard-Jones interactions; I have turned charges off by setting
Re: [gmx-users] umbrella sampling using replica exchange
Sanku M wrote: Hi, I was wondering whether in gromacs 4, one can use replica exchange simulation in combination with umbrella sampling. In theory, yes. Whether or not it is efficient or stable is perhaps another matter. -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
[gmx-users] Total Kinetic Energy And Rotational And Translational Kinetic Energy
Hi, there, I am doing a very simple case of a ice cubic box. I would like to use g_energy to investigate the total kinetic energy of the system and use g_traj to generate the rotational and translational kinetic energy separately, by -ekr and -ekt flags. However I found that the sum of the rotational and translational kinetic energy is not equal to the generated total kinetic energy. At first I thought this might be because the temperature was so low and constricted the motions of molecules, then I made a new system of a water cubic box in 300 K. However, the result was the same, i.e. the total KE and the sum of rotational KE and translational KE was not the same, and actually their gap was kind of large. I totally have no idea about this. Is there something wrong or something I missed? Many thanks, Size Zheng-- 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
