Re: [gmx-users] Glycoproteion MD
Dear (sorry cant read chinese), You can find some OPLS or 53a6 Parameters on the web by doing extensive searches, mostly they are free, but hosted on varied individual lab web sites. That, or it may be easier to define some sets of bonds (angles, dihedrials, lengths charges, etc...from either the CRC or national institute of standards) for a small subset of sugars, inclusive of the inter-chain bonds, and then just use the defined names you gave the sugar atoms (ie Cc for sugar carbon, Pc for phosphorylated to sugar, etc... as inclusive this would only be several to a dozen atom types or somthing)(then you can post it :-))...but it might be easier than trying to define things based on single sugar moieties available on the web, as you most likely would have errors when your suger moities are large from the inter-sugar bonds between subunits, such as a 10-20 length polysacharide on a glycosylated protein. This is less trivial than it might seem, but would still take a few days, and you might be able to use all but say 1-2 atoms if you find several defined parameters for sugars on the web already... Sincerely, Stephan Watkins Original-Nachricht Datum: Fri, 31 Aug 2012 09:26:38 +0800 Von: 陈应广 525342...@qq.com An: gmx-users gmx-users@gromacs.org Betreff: [gmx-users] Glycoproteion MD Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Thanking all -- 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] Umbrella Sampling Pull code Problem
Dear Gromacs users, I have encountered a strange problem when trying to set up umbrella sampling simulations using gromacs 4.5.3. My system contains two groups with a COM distance of 1.95 nm (all distances measured by g_dist). Trying to set up the first US window, I use the following pull code, together with typical mdp parameters from the Gromacs US tutorial: ; pull options pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = yes pull_init1 = 0.00 pull_nstxout= 1 pull_nstfout= 0 pull_group0 = Protein pull_group1 = OHM pull_rate1 = 0.0 pull_k1 = 1 this results in a simulation in which the group distance remains close to 1.95nm, as expected. However, when I make the following two changes in my input file: pull_start = no pull_init1 = 1.95 which should (?) amount to an equivalent setup, a very different trajectory results in which the COM distance quickly increases to 2.7 nm and then appears to be restrained there. (Visualization confirms, in the first case, the groups remain in their starting conformation, in the second one, they are pushed appart) Interestingly, the grompp output contains the following lines: Pull group natoms pbc atom distance at start reference at t=0 0 994 497 1 2 46347 1.224 1.950 in this case. Apparently, grompp (and mdrun thereafter) calculates the group COM distance differently from g_dist! I think this is not a PBC issue, every atomic distance within both groups is smaller than half the box size and the pbcatoms are close together. However, when I set pbcatom0 to various atom numbers, different 'distance at start' values are obtained, but never the correct COM distance. The two groups do not have overlapping atoms. I am sure I used the same group indexes for pulling and distance measurements. This behaviour is so visibly wrong that I cannot believe this is a bug and rather think I am doing something incorrect. A search of the list revealed a somewhat similar report by Gavin Melaugh in 2011 which did not resolve the issue. Any ideas on what might be the problem here? I am willing to send around files to reproduce the problem of course. Thomas Dr. Thomas Steinbrecher Institut für Physikalische Chemie, KIT Kaiserstr. 12, 76131 Karlsruhe-- 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] Glycoproteion MD
Thanks for your help ,you can call me Guang.I come from China. -- -- ??: lloyd riggslloyd.ri...@gmx.ch; : 2012??8??31??(??) 7:25 ??: Discussion list for GROMACS usersgmx-users@gromacs.org; : Re: [gmx-users] Glycoproteion MD Dear (sorry cant read chinese), You can find some OPLS or 53a6 Parameters on the web by doing extensive searches, mostly they are free, but hosted on varied individual lab web sites. That, or it may be easier to define some sets of bonds (angles, dihedrials, lengths charges, etc...from either the CRC or national institute of standards) for a small subset of sugars, inclusive of the inter-chain bonds, and then just use the defined names you gave the sugar atoms (ie Cc for sugar carbon, Pc for phosphorylated to sugar, etc... as inclusive this would only be several to a dozen atom types or somthing)(then you can post it :-))...but it might be easier than trying to define things based on single sugar moieties available on the web, as you most likely would have errors when your suger moities are large from the inter-sugar bonds between subunits, such as a 10-20 length polysacharide on a glycosylated protein. This is less trivial than it might seem, but would still take a few days, and you might be able to use all but say 1-2 atoms if you find several defined parameters for sugars on the web already... Sincerely, Stephan Watkins Original-Nachricht Datum: Fri, 31 Aug 2012 09:26:38 +0800 Von: ?? 525342...@qq.com An: gmx-users gmx-users@gromacs.org Betreff: [gmx-users] Glycoproteion MD Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Thanking all -- 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
Re: [gmx-users] Glycoproteion MD
Hi, If you can't find parameters for glycoprotein's MD for charmm27, OPLS or Amber99 (and GROMOS is an alternative for you), we've been working on MD simulations with this class of biomolecules, using GROMOS96 43A1 force field, as described: Pol-Fachin, L.; Fernandes, C.L.; Verli, H.: GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations. Carbohydrate Research 344 (2009) 491–500. Fernandes, C.L.; Sachett, L.G.; Pol-Fachin, L.; Verli, H.: GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins. Carbohydrate Research 345 (2010) 663–671. Best regards, Laércio Pol-Fachin - Message: 1 Date: Thu, 30 Aug 2012 21:32:00 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Glycoproteion MD To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50401410.7070...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed On 8/30/12 9:26 PM, 陈应广 wrote: Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where else I should search for these. If they haven't already been derived (and thus likely published), then you'll have to derive them yourself in a manner consistent with the original force field. http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Umbrella Sampling Pull code Problem
I have met similar problem before. The distance calculated by g_dist is different from that calculated by grommp, especially when the actual distance between the two groups is very small. As the actual distance becomes larger, the difference of the distance from the two commands becomes smaller. In addition, in my case, when using larger box size, the difference gets smaller. I don't know why, but you may try to use larger box size to minimize the difference. I am also curious of what is the reason. -- Jianguo - Original Message - From: Steinbrecher, Thomas (IPC) thomas.steinbrec...@kit.edu To: gmx-users@gromacs.org gmx-users@gromacs.org Cc: Sent: Friday, 31 August 2012, 19:45 Subject: [gmx-users] Umbrella Sampling Pull code Problem Dear Gromacs users, I have encountered a strange problem when trying to set up umbrella sampling simulations using gromacs 4.5.3. My system contains two groups with a COM distance of 1.95 nm (all distances measured by g_dist). Trying to set up the first US window, I use the following pull code, together with typical mdp parameters from the Gromacs US tutorial: ; pull options pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = yes pull_init1 = 0.00 pull_nstxout = 1 pull_nstfout = 0 pull_group0 = Protein pull_group1 = OHM pull_rate1 = 0.0 pull_k1 = 1 this results in a simulation in which the group distance remains close to 1.95nm, as expected. However, when I make the following two changes in my input file: pull_start = no pull_init1 = 1.95 which should (?) amount to an equivalent setup, a very different trajectory results in which the COM distance quickly increases to 2.7 nm and then appears to be restrained there. (Visualization confirms, in the first case, the groups remain in their starting conformation, in the second one, they are pushed appart) Interestingly, the grompp output contains the following lines: Pull group natoms pbc atom distance at start reference at t=0 0 994 497 1 2 46347 1.224 1.950 in this case. Apparently, grompp (and mdrun thereafter) calculates the group COM distance differently from g_dist! I think this is not a PBC issue, every atomic distance within both groups is smaller than half the box size and the pbcatoms are close together. However, when I set pbcatom0 to various atom numbers, different 'distance at start' values are obtained, but never the correct COM distance. The two groups do not have overlapping atoms. I am sure I used the same group indexes for pulling and distance measurements. This behaviour is so visibly wrong that I cannot believe this is a bug and rather think I am doing something incorrect. A search of the list revealed a somewhat similar report by Gavin Melaugh in 2011 which did not resolve the issue. Any ideas on what might be the problem here? I am willing to send around files to reproduce the problem of course. Thomas Dr. Thomas Steinbrecher Institut für Physikalische Chemie, KIT Kaiserstr. 12, 76131 Karlsruhe-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Umbrella Sampling Pull code Problem
On Fri, Aug 31, 2012 at 1:45 PM, Steinbrecher, Thomas (IPC) thomas.steinbrec...@kit.edu wrote: However, when I make the following two changes in my input file: pull_start = no pull_init1 = 1.95 which should (?) amount to an equivalent setup, a very different trajectory results in which the COM distance quickly increases to 2.7 nm and then appears to be restrained there. (Visualization confirms, in the first case, the groups remain in their starting conformation, in the second one, they are pushed appart) My guess is that you should use -1.95 as pull_init1 (mind the minus sign) and that the COM distance you measure is actually close to 2.9 nm (which is 1.95*2). g_dist measures a distance which is always non-negative, however pull_init1 is used as a reference position so its sign depends on the geometry of pulling. Cheers, Bogdan -- 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] Turning off electrostatics between groups using custom tables?
Hi, I've been trying to turn off the electrostatic interaction between two groups (an ion-group and protein) by following the tutorial on custom table generation, but have seemed to have hit a road block. Looking at the structure of the sample 6-12 table provided in the topology directory, I constructed my table.xvg for interactions between the two groups to be the following: #r coulomb coulomb-force 1/r^6 6/ r^7 1/12 12/r^13 00 0 0 0 0 0 . 0.04 0 0 -2.4414062500e+08 -3.6621093750e+10 5.9604644775e+16 1.7881393433e+19 and so on. Noting that the second and third columns are defined as zero for all steps, while the columns related to LJ are left unchanged. While for the protein-protein or ion-group ion-group interactions I provide just the standard 6-12 table. The problem comes that when I run using my modified table, the system will run but gradually explodes. I note that when I look back at my output from grompp I find a warning concerning eplison and sigma being used instead of C6 and C12, but if I swap my custom table for the sample 6-12 table (keeping the first two columns not zero) the system doesn't explode and has dynamics similar to previous simulations making use the built-in table generation. Any ideas on where I am going wrong? Here are the other specs for the simulations: Gromacs 4.0.5, OPLS/AA, berendsen pressure/temperature coupling: tau_p =0.5, tau_t=0.1, simulation temperature 283. Any help is much appreciated! -Smitty -- View this message in context: http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Umbrella Sampling Pull code Problem
As Bogdan suggested this could be an issue with the sign of the distance. When you run grompp you get Pull group natoms pbc atom distance at start reference at t=0 0 994 497 1 2 46347 1.224 1.950 which suggests your starting structure is at 1.22 nm but it could be +/- 1.224 nm you might want to manually check the distance for your starting structure. Gromacs restraints does not distinguish the sign of the distance so when u started running the simulation, since you have a huge force constant of 1 kJ/mol, the pulling group is pulled to the window distance of 1.95 except that it could be -1.95 instead of +1.95 resulting in a COM distance around 2.7 nm. I had a similar problem when I tried pulling a peptide into the bilayer with the reference group being the center of mass of the bilayer. For the window at 0.5 nm, my starting structure had the pull group around -0.5 nm which I did not notice was off by 1 nm since I had used g_dist to check the distances. However the simulations ran fine with the pullx file listing distances around -0.5 nm. This should not ideally happen if the restraining section of gromacs distinguishes postive and negative distances because if it did, then the peptide would have been pulled to the window distance of 0.5 nm within the first few ps of the simulation. I used 'pull_geometry = distance' and I think gromacs restrains the pull_group at the magnitude of the distance although the pullx file lists negative distances. My understanding is that it will make no difference whether you give +1.95 or -1.95 for the pull_init1 unless your starting conformations have the distances at +1.95 and -1.95 respectively. Also another problem I had with negative distances is that g_wham does not distinguish the sign of the distances so even if the pullx file has negative values the pmf will be given only for the magnitude of the distances which is not what you want. So it will be best if you can choose a reference group such that the distance between your pull group and the reference is always positive. For my case I used the center of mass of the phosphate atoms in the lower leaflet of the bilayer as the reference group to pull the peptide into the bilayer instead of using the center of mass of the bilayer. The important thing is also to manually check the distance between ur pull and ref groups for the starting structures and start from a structure very close to the window position especially with large force constants so you can avoid sudden pulling for the pull groups. Please note, I used Gromacs 4.0.5 for my umbrella sampling simulations and I am not sure if what I observed is applicable to version 4.5.3. Sheeba - Sheeba J. Irudayam Postdoctoral Researcher Department of Chemistry University of North Carolina at Chapel Hill isheeba[at]email.unc.edu -- View this message in context: http://gromacs.5086.n6.nabble.com/Umbrella-Sampling-Pull-code-Problem-tp5000715p5000725.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Turning off electrostatics between groups using custom tables?
On 1/09/2012 1:14 AM, Smitty wrote: Hi, I've been trying to turn off the electrostatic interaction between two groups (an ion-group and protein) by following the tutorial on custom table generation, but have seemed to have hit a road block. Looking at the structure of the sample 6-12 table provided in the topology directory, I constructed my table.xvg for interactions between the two groups to be the following: #r coulomb coulomb-force 1/r^6 6/ r^7 1/12 12/r^13 00 0 0 0 0 0 . 0.04 0 0 -2.4414062500e+08 -3.6621093750e+10 5.9604644775e+16 1.7881393433e+19 and so on. Noting that the second and third columns are defined as zero for all steps, while the columns related to LJ are left unchanged. While for the protein-protein or ion-group ion-group interactions I provide just the standard 6-12 table. The problem comes that when I run using my modified table, the system will run but gradually explodes. I note that when I look back at my output from grompp I find a warning concerning eplison and sigma being used instead of C6 and C12, Ignoring warnings is a great way to waste time, and if you can't provide specific details of what it was, you're unlikely to get specific help. but if I swap my custom table for the sample 6-12 table (keeping the first two columns not zero) the system doesn't explode and has dynamics similar to previous simulations making use the built-in table generation. Any ideas on where I am going wrong? Can't tell. What's the ion group? Does it even get close to Protein? Mark Here are the other specs for the simulations: Gromacs 4.0.5, OPLS/AA, berendsen pressure/temperature coupling: tau_p =0.5, tau_t=0.1, simulation temperature 283. Any help is much appreciated! -Smitty -- View this message in context: http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Turning off electrostatics between groups using custom tables?
While for the protein-protein or ion-group ion-group interactions I provide just the standard 6-12 table. The problem comes that when I run using my modified table, the system will run but gradually explodes. I note that when I look back at my output from grompp I find a warning concerning eplison and sigma being used instead of C6 and C12, Ignoring warnings is a great way to waste time, and if you can't provide specific details of what it was, you're unlikely to get specific help. The warning is as follows: WARNING 1 [file pep_ion.top, line 1218]: Using sigma/epsilon based combination rules with user supplied potential function may produce unwanted results. I've looked into this on the mailing list, but it appears that so long as the forces are what I expect them to using the standard tables, I should be able to ignore this warning. Hopefully I have not misread the previous threads. but if I swap my custom table for the sample 6-12 table (keeping the first two columns not zero) the system doesn't explode and has dynamics similar to previous simulations making use the built-in table generation. Any ideas on where I am going wrong? Can't tell. What's the ion group? Does it even get close to Protein? The ion group is a set of 50 dissociated ions (25 K+, 25 Cl-). The ions under standard simulation conditions (non-custom interaction table) rarely have K+ or Cl- atoms coming within 0.5 angstroms of any atom of the protein group; but they do still happen. If it helps my .mdp file for the simulation is attached. http://gromacs.5086.n6.nabble.com/file/n5000727/md.mdp md.mdp Thanks again, hope this clears up my question. -Smitty -- View this message in context: http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723p5000727.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Glycoproteion MD
Hi Guang, You can use the GLYCAM force field, which has parameters for carbohydrates and glycoproteins compatible with AMBER99. You can get the AMBER topology and structure files directly from their web interface, the Online Glycoprotein Builder ( http://glycam.ccrc.uga.edu/ccrc/gp/ http://glycam.ccrc.uga.edu/ccrc/), and them convert it to .top and .gro with the acpype script. I've done it sometimes. I hope it is helpful for you. best regards, Leandro 2012/8/30 陈应广 525342...@qq.com Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Thanking all -- 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
Re: [gmx-users] Elastic network model
Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 3 1 1 5.10184956658 61.9 3 2 1 3.69916125628 61.9 4 1 1 4.19781502689 61.9 4 2 1 5.90237528458 61.9 4 3 1 3.92569102197 61.9 5 1 1 5.30324730708 61.9 5 3 1 5.269426249661.9 5 4 1 3.83092403997 61.9 6 3 1 4.07288043036 61.9 6 4 1 5.48720921781 61.9 6 5 1 3.71358990735 61.9 7 3 1 5.51608248669 61.9 7 6 1 3.868286571661.9 8 7 1 3.804772135161.9 9 8 1 3.81975719124 61.9 10 9 1 3.72026195314 61.9 11 10 1 3.76893910802 61.9 12 11 1 3.812386522961.9 13 12 1 3.78850801768 61.9 14 13 1 3.69171193351 61.9 15 13 1 5.42834818338 61.9 15 14 1 3.83449357804 61.9 16 13 1 5.10757946585 61.9 16 15 1 3.83922544272 61.9 17 11 1 5.71881902144 61.9 17 12 1 4.83263696133 61.9 17 13 1 5.48196032456 61.9 The above one is part of topology file. I have 372 residues in my protein. when i run equilibration i got the following error A list of missing interactions: Bond . of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. None of the interactions are repeated multiple times, when i check the log file the following error is written Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond. of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Error Can you suggest me what does this error mean . Is the topology correct (built) with respect to elastic network model. Thank you, Mohan On Thu, Aug 30, 2012 at 5:58 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi , Thank you very much .I will take all these factors in to account while building the model. Thank you, Mohan. On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 30/08/2012 10:17 PM, Mark Abraham wrote: On 30/08/2012 10:02 PM, mohan maruthi sena wrote: Hi, I am going through it , i will understand it and try to build the topology. Fundamentally, harmonic bonds do not serve your purpose, since you need an interaction that is harmonic in the change in distance, not harmonic in the distance. Hence your problems with collapsing systems. As such, you want to look at using distance restraints, rather than [bonds]. On second thoughts, a sufficient network of harmonic bonds can suffice, but you need to embed the distance in the topology. [distance_restraints] are just easier because you can let the initial structure determine the equilibrium position. (Unless you don't want that) Mark Mark Thank you, Mohan On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On
Re: [gmx-users] Elastic network model
On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 Less than 6 Angstrom ??? You need to read the topology chapter of the manual again. And then again. It will save you lots of time later. Hint: some units are wrong. Good luck! Bogdan -- 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: Force fields, is there a review article?
Thank you, Luca, for the link to the Ponder and Case review article. http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf It is indeed the kind of article I have been seeking. maybe one of the best thing to do is to test the FF vs experimental data and check which one reproduces them better or provides more stability. Ah well, that won't help me. In my case, the molecular dynamics simulations are what will be used to justify an experimental investigation! -- View this message in context: http://gromacs.5086.n6.nabble.com/Force-fields-is-there-a-review-article-tp5000519p5000732.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Elastic network model
GROMACS uses nm as the unit of length, so this is 38 Angstroms, shouldn't be a problem. On 2012-08-31, at 2:23 PM, Bogdan Costescu bcoste...@gmail.com wrote: On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 Less than 6 Angstrom ??? You need to read the topology chapter of the manual again. And then again. It will save you lots of time later. Hint: some units are wrong. Good luck! Bogdan -- 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
Re: [gmx-users] Elastic network model
On 1/09/2012 4:42 AM, mohan maruthi sena wrote: Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 3 1 1 5.10184956658 61.9 3 2 1 3.69916125628 61.9 4 1 1 4.19781502689 61.9 4 2 1 5.90237528458 61.9 4 3 1 3.92569102197 61.9 5 1 1 5.30324730708 61.9 5 3 1 5.269426249661.9 5 4 1 3.83092403997 61.9 6 3 1 4.07288043036 61.9 6 4 1 5.48720921781 61.9 6 5 1 3.71358990735 61.9 7 3 1 5.51608248669 61.9 7 6 1 3.868286571661.9 8 7 1 3.804772135161.9 9 8 1 3.81975719124 61.9 10 9 1 3.72026195314 61.9 11 10 1 3.76893910802 61.9 12 11 1 3.812386522961.9 13 12 1 3.78850801768 61.9 14 13 1 3.69171193351 61.9 15 13 1 5.42834818338 61.9 15 14 1 3.83449357804 61.9 16 13 1 5.10757946585 61.9 16 15 1 3.83922544272 61.9 17 11 1 5.71881902144 61.9 17 12 1 4.83263696133 61.9 17 13 1 5.48196032456 61.9 The above one is part of topology file. I have 372 residues in my protein. when i run equilibration i got the following error A list of missing interactions: Bond . of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. None of the interactions are repeated multiple times, when i check the log file the following error is written Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond. of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Error Can you suggest me what does this error mean . Is the topology correct (built) with respect to elastic network model. It means your system is http://www.gromacs.org/Documentation/Terminology/Blowing_Up. Maybe your velocities are far too large for your tiny bond stiffness constants, or your integration step was too large, or probably a dozen other things we can only guess at because we don't know your initial configuration or your .mdp file contents. If you're just inventing stuff on your own, then I suggest you find an actual elastic network model of which someone else has already published a dynamical model, and work out how to implement that, instead of hoping someone will tell you how an actual elastic network model works. Only then do you have some basis for seeking to do something novel. 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] Re: Turning off electrostatics between groups using custom tables?
On 1/09/2012 2:50 AM, Smitty wrote: While for the protein-protein or ion-group ion-group interactions I provide just the standard 6-12 table. The problem comes that when I run using my modified table, the system will run but gradually explodes. I note that when I look back at my output from grompp I find a warning concerning eplison and sigma being used instead of C6 and C12, Ignoring warnings is a great way to waste time, and if you can't provide specific details of what it was, you're unlikely to get specific help. The warning is as follows: WARNING 1 [file pep_ion.top, line 1218]: Using sigma/epsilon based combination rules with user supplied potential function may produce unwanted results. I've looked into this on the mailing list, but it appears that so long as the forces are what I expect them to using the standard tables, I should be able to ignore this warning. Hopefully I have not misread the previous threads. but if I swap my custom table for the sample 6-12 table (keeping the first two columns not zero) the system doesn't explode and has dynamics similar to previous simulations making use the built-in table generation. Any ideas on where I am going wrong? Can't tell. What's the ion group? Does it even get close to Protein? The ion group is a set of 50 dissociated ions (25 K+, 25 Cl-). The ions under standard simulation conditions (non-custom interaction table) rarely have K+ or Cl- atoms coming within 0.5 angstroms of any atom of the protein group; but they do still happen. If it helps my .mdp file for the simulation is attached. http://gromacs.5086.n6.nabble.com/file/n5000727/md.mdp md.mdp 1) That .mdp applies different tables to K-K, protein-protein and all other interactions, which isn't what you've said you've done. 2) You should follow the advice here http://www.gromacs.org/Documentation/Terminology/Thermostats 3) Your life will be simpler if you use energygrp_table only for the group-group interactions you want to change, and leave the default interactions normal. It will also be faster, because using tabulated interactions is much slower than the normal ones. 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] Hydrogen bond breaking process
Can you tell me how to predict the Hydrogen bond breaking process (For example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD simulation? Kind regards Rajiv -- 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
