Re: [gmx-users] Periodic Images - clarification
Hi Kavya, I did use dodecahedron cell. but how does using a dodecahedron cell be advantageous than any other cell when minimum image violation has occurred? This is just my inquisitiveness. In a rectangular cell, such interactions may occur merely by reorientation of the solute. In that case it is likely that self-interactions over PBC have a persistent effect on the dynamics. And when I was visualizing the trajectory in VMD along with other periodic images in +/-X, +/-Y and +/-Z directions I saw only 26images, this is good for a cubic cell. But how can I visualize a dodecahedron cell? Which has more faces --- more periodic images (If I am not wrong) than a cubic or rectangular cell.. Actually, there are less. A rhombic dodecahedron has 12 neighbours. A cubic/rectangular cell has 6 faces, but for those you also have to consider the neighbours at the edges and corners, which brings the total to 26. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] placing dihedral constraints
Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks.-- 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] placing dihedral constraints
On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote: Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks. See http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints to sort out some nomenclature. You probably want a dihedral restraint with a strong force constant (though other approaches are possible). See relevant parts of chapters 4 and 5. Work by analogy from the [dihedrals] and [position_restraints] sections in your existing [moleculetype]. 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] missing topology file adn creating a new one
Dear all, i am doing a sampling method and in a stage of completion But unfortunatelymy topol.top file is missing and am really helpless .i cant continue the simulation.i have the tpr file adn pdb file at last step.i tried to create the top file from *g_x2top -f beta_md17.tpr -o topol.top -ff select* when it prompts for a force field i selected charmm27 which is what i used for the simulation it give me the following error Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) --- Program g_x2top, VERSION 4.5.3 Source code file: g_x2top.c, line: 505 Fatal error: No or incorrect atomname2type.n2t file found (looking for charmm27.ff) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors i* tried to use pdb2gmx as well pdb2gmx -f 2.pdb -o 2.gro -p topool.top * End terminus GLU-56: COO- Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/aminoacids.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/dna.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/rna.arn Checking for duplicate atoms Now there are 16 residues with 247 atoms Chain time... Making bonds... Number of bonds was 250, now 250 Generating angles, dihedrals and pairs... Before cleaning: 649 pairs Before cleaning: 654 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 14 cmap torsion pairs There are 654 dihedrals, 35 impropers, 444 angles 640 pairs, 250 bonds and 0 virtual sites Total mass 1860.928 a.m.u. Total charge -3.000 e Writing topology Processing chain 2 (3 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue NA2139 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2140 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2141 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'NA' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- 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] missing topology file adn creating a new one
sreelakshmi ramesh wrote: Dear all, i am doing a sampling method and in a stage of completion But unfortunatelymy topol.top file is missing and am really helpless .i cant continue the simulation.i have the tpr file adn pdb file at last step.i tried to create the top file from *g_x2top -f beta_md17.tpr -o topol.top -ff select* when it prompts for a force field i selected charmm27 which is what i used for the simulation it give me the following error Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) --- Program g_x2top, VERSION 4.5.3 Source code file: g_x2top.c, line: 505 Fatal error: No or incorrect atomname2type.n2t file found (looking for charmm27.ff) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors i* tried to use pdb2gmx as well pdb2gmx -f 2.pdb -o 2.gro -p topool.top * End terminus GLU-56: COO- Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/aminoacids.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/dna.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/rna.arn Checking for duplicate atoms Now there are 16 residues with 247 atoms Chain time... Making bonds... Number of bonds was 250, now 250 Generating angles, dihedrals and pairs... Before cleaning: 649 pairs Before cleaning: 654 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 14 cmap torsion pairs There are 654 dihedrals, 35 impropers, 444 angles 640 pairs, 250 bonds and 0 virtual sites Total mass 1860.928 a.m.u. Total charge -3.000 e Writing topology Processing chain 2 (3 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue NA2139 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2140 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2141 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'NA' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors pdb2gmx is ill-suited for dealing with multiple molecules. You haven't said what's in your system, but if it's something simple like a protein in water with ions, it's trivial to re-create a topology. Just run pdb2gmx on the protein only, then manually add the missing water and ions to the topology. If you're system is something more complex than that, then hopefully you've documented your procedure well such that you can reproduce it. And don't let files go missing :) -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] Periodic Images - clarification
Dear Sir Thanks I got the point! Thanking you With Regards M. Kavyashree On Mon, Jun 27, 2011 at 12:19 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Kavya, I did use dodecahedron cell. but how does using a dodecahedron cell be advantageous than any other cell when minimum image violation has occurred? This is just my inquisitiveness. In a rectangular cell, such interactions may occur merely by reorientation of the solute. In that case it is likely that self-interactions over PBC have a persistent effect on the dynamics. And when I was visualizing the trajectory in VMD along with other periodic images in +/-X, +/-Y and +/-Z directions I saw only 26images, this is good for a cubic cell. But how can I visualize a dodecahedron cell? Which has more faces --- more periodic images (If I am not wrong) than a cubic or rectangular cell.. Actually, there are less. A rhombic dodecahedron has 12 neighbours. A cubic/rectangular cell has 6 faces, but for those you also have to consider the neighbours at the edges and corners, which brings the total to 26. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] g_msd bug
Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With time of calculations the memory reserves are gradually devoured to the extent, in my case, of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps in memory. Have you heard of such case? Best wishes, Slawomir-- 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_msd bug
Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 Sławomir Stachura stachura.slawo...@gmail.com: Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With time of calculations the memory reserves are gradually devoured to the extent, in my case, of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps in memory. Have you heard of such case? Best wishes, Slawomir-- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Comparing MD ensembles with exp. NOE restraints -- bus error
Hi There, I would like to compare my ensemble of (unrestrained) MD structures against experimental NOE distances. For that, I have added the distance_restraints block to my *.top file such as: [distance_restraints] ;aiaj type index type’ low up1 up2 fac 3331101 0.0 3.000 1.2 0.4 3531111 0.0 2.500 0.7 0.3 I have also added the disre options below to the *.mdp file used to generate a new tpr for the NOE analysis disre = Simple disre-weighting = Equal disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 1 When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives a bus error ... I am copying the entire mdp file in case someone can point me out what is wrong with it. I would appreciate any suggestions on what maybe wrong here, Cheers, Thereza integrator = md dt = 0.002 nsteps = 2500 nstxout = 500 nstvout = 500 nstlog = 500 nstenergy= 500 nstxtcout= 500 comm-mode= Linear nstcomm = 5 comm-grps= SYSTEM xtc_grps = SYSTEM energygrps = SYSTEM nstlist = 5 rlist= 1.4 coulombtype = generalized-reaction-field epsilon_rf = 66.0 ns_type = grid rcoulomb = 1.4 rvdw = 1.4 pbc = xyz tcoupl = berendsen tc-grps = SYSTEM tau_t= 0.2 ref_t= 300 Pcoupl = berendsen Pcoupltype = semi-isotropic tau_p= 0.4 0.4 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 gen_vel = yes gen_temp = 10 gen_seed = 178296 constraints = h-bonds disre = simple disre-weighting = equal disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 1 -- 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] Comparing MD ensembles with exp. NOE restraints -- bus error
Thereza Soares wrote: Hi There, I would like to compare my ensemble of (unrestrained) MD structures against experimental NOE distances. For that, I have added the distance_restraints block to my *.top file such as: [distance_restraints] ;aiaj type index type’ low up1 up2 fac 3331101 0.0 3.000 1.2 0.4 3531111 0.0 2.500 0.7 0.3 I have also added the disre options below to the *.mdp file used to generate a new tpr for the NOE analysis disre = Simple disre-weighting = Equal disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 1 When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives a bus error ... I am copying the entire mdp file in case someone can point me out what is wrong with it. There is nothing wrong with the .mdp file. There is likely a bug in the g_disre code somewhere, as is usually the case with immediate bus errors or segmentation faults. I would appreciate any suggestions on what maybe wrong here, You haven't mentioned which version of Gromacs you're using, but if it is not 4.5.4 (the latest), please try again with this version. If you are using 4.5.4 or the error persists, please file an issue report on redmine.gromacs.org and include your .tpr and .pdb files necessary to reproduce the problem. -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_msd bug
Hello, thank you for your reply. I have used following command : g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4. Indeed my network administrator was very unhappy about comsumed memory. Regards, Slawomir Wiadomość napisana przez Tsjerk Wassenaar w dniu 2011-06-27, o godz. 15:40: Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 Sławomir Stachura stachura.slawo...@gmail.com: Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With time of calculations the memory reserves are gradually devoured to the extent, in my case, of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps in memory. Have you heard of such case? Best wishes, Slawomir-- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] about periodic images violation
Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a model. I made several simulations changing the gen_seed in order to explore deeply the conformational space of the protein. I used a triclinic box (option editconf -bt triclinic -d 1 -c) filled with spc water and neutralized with ions; in my opinion, it's quite a standard system. I equilibrated the system with a minimization (emtol = 500 reached) and with NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the full MD for 30 ns, always at 310 K. I repeated this procedure (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers), starting from the same minimized structure. Obviously, in PR-NPT and full Md simulations, I did not recalculated the initial velocity (it's a continuation). Before starting with full MD I checked for energetic parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no apparent problems. I run the 30 ns simulations and now I'm checking for the results. Looking at the trajectories I see that in some (but not all) cases, the protein moves from the center of the box to one of the edges, starting from a time that is different in each simulation, when it happens. I run g_mindist, and in some cases (generally when the protein doesn't move so much) I see some spikes in the plot (that disappear if I apply trjconv -pbc nojump to the trajectory), but apart from these spikes the minimum periodic distance in the trajectory is at least 1.5 nm (I set van der Waals cut-off at 1.4 nm). In other cases, however (essentially when the protein starts moving towards the edges of the box), the minimum periodic distance starts decreasing (in some simulations after 10 ns, in some simulations after 20: there is not a common point after which you can see a sudden decrease of minimum periodic distance of the system) and reaches a value below 1.4 nm or even below 1 nm. Considering that the starting system is more or less the same in all cases, I don't identify the reason why the system behaves like this, and moreover what can I do to avoid this. My questions are: - do I have to enlarge the box? but I don't think that this would solve the motion of the protein towards one edge of the box - do I have to change the box? In his last message Tsjerk suggests to use a rhombic dodecahedron box, could it be useful in my case? - do you think it's a problem of stabilization of the system? Should I run a deeper minimization, or a longer NVT+NPT in my system? I'm quite puzzled especially because the system is the same in all cases, the only thing I changed in my simulations is the gen_seed. Could anybody give me some suggestions about it? Thank you very much Anna -- 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] Regarding NPT Eq.
Dear All, I have been trying to do NPT equilibration for 100 ps. I have tried with different tau_p like from 0.5 to 2 and my reference pressure is 1 bar. Since I am continuing from 20 ps NVT equilibrated configuration, in npt.mdp I have written init_step = 1 (1*0.02 fs = 20 ps). But instead of doing all this I am not able equilibrate to 1 bar. Is there any thing wrong in my formalism. Please let me. Thank you in advance. -- 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] about periodic images violation
Hi Anna, The spikes you see occur because the protein is broken over the periodic boundaries. Not hard to see that a broken molecule will have a minimal minimal distance. The other problem may well occur due to rotation of your molecule. Since you set -bt tric, you just get a rectangular unit cell, which has the drawback that the shortest distance may not be long enough to keep the protein from self-interactions in certain orientations. I know it's considered a pretty standard setup, which is why I mentioned it before. You should use a rhombic dodecahedron. With a rectangular cell, you could even have self-interaction in a nastier way: the ends of the protein can try to avoid each other, rather than align with each other. That would result in an altered ensemble, yet one in which you wouldn't see violations of the minimal distance. In a rhombic dodecahedron the spatial distribution is much more uniform... Cheers, Tsjerk On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a model. I made several simulations changing the gen_seed in order to explore deeply the conformational space of the protein. I used a triclinic box (option editconf -bt triclinic -d 1 -c) filled with spc water and neutralized with ions; in my opinion, it's quite a standard system. I equilibrated the system with a minimization (emtol = 500 reached) and with NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the full MD for 30 ns, always at 310 K. I repeated this procedure (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers), starting from the same minimized structure. Obviously, in PR-NPT and full Md simulations, I did not recalculated the initial velocity (it's a continuation). Before starting with full MD I checked for energetic parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no apparent problems. I run the 30 ns simulations and now I'm checking for the results. Looking at the trajectories I see that in some (but not all) cases, the protein moves from the center of the box to one of the edges, starting from a time that is different in each simulation, when it happens. I run g_mindist, and in some cases (generally when the protein doesn't move so much) I see some spikes in the plot (that disappear if I apply trjconv -pbc nojump to the trajectory), but apart from these spikes the minimum periodic distance in the trajectory is at least 1.5 nm (I set van der Waals cut-off at 1.4 nm). In other cases, however (essentially when the protein starts moving towards the edges of the box), the minimum periodic distance starts decreasing (in some simulations after 10 ns, in some simulations after 20: there is not a common point after which you can see a sudden decrease of minimum periodic distance of the system) and reaches a value below 1.4 nm or even below 1 nm. Considering that the starting system is more or less the same in all cases, I don't identify the reason why the system behaves like this, and moreover what can I do to avoid this. My questions are: - do I have to enlarge the box? but I don't think that this would solve the motion of the protein towards one edge of the box - do I have to change the box? In his last message Tsjerk suggests to use a rhombic dodecahedron box, could it be useful in my case? - do you think it's a problem of stabilization of the system? Should I run a deeper minimization, or a longer NVT+NPT in my system? I'm quite puzzled especially because the system is the same in all cases, the only thing I changed in my simulations is the gen_seed. Could anybody give me some suggestions about it? Thank you very much Anna -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
[gmx-users] g_msd bug
600 GB of memory? I highly doubt that you have that much memory available. Are you sure that this is not a typo? Can you please post evidence that you have =600 GB of memory available? It is common for clusters to disallow an individual process from using 10% of the total memory on a head-node, which makes 600 MB more likely, in which case you can try submitting your job to a compute node. -- original message -- Hello, thank you for your reply. I have used following command : g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4. Indeed my network administrator was very unhappy about comsumed memory. Regards, Slawomir Wiadomo¶æ napisana przez Tsjerk Wassenaar w dniu 2011-06-27, o godz. 15:40: [Hide Quoted Text] Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 S³awomir Stachura stachura.slawo...@gmail.com: Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With time of calculations the memory reserves are gradually devoured to the extent, in my case, of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps in memory. Have you heard of such case? Best wishes, -- 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] Regarding NPT Eq.
Hi What do you mean with not being able to equilibrate to 1 bar? Could you please post g_energy output and which pressure coupling scheme are you using? Keep in mind that pressure suffers from large oscillations (http://www.gromacs.org/Documentation/Terminology/Pressure). Also, depending on the size of your system, 100 ps might be not enough to equilibrate the pressure. El 27/06/11 16:50, Ravi Kumar Venkatraman escribió: Dear All, I have been trying to do NPT equilibration for 100 ps. I have tried with different tau_p like from 0.5 to 2 and my reference pressure is 1 bar. Since I am continuing from 20 ps NVT equilibrated configuration, in npt.mdp I have written init_step = 1 (1*0.02 fs = 20 ps). But instead of doing all this I am not able equilibrate to 1 bar. Is there any thing wrong in my formalism. Please let me. Thank you in advance. -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- 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] minimization problem
Dear Gromacs users and developers, I'm trying to set up simulation. I have a big simulation of something like half million atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax 10 I tried to use a bigger emtol(emtol=20) and it still didn't converge.However I still run the MD with dt = 0.03 and nstxout = 1. after something like 100 steps the system blow up. I will appreciate any help with this issue. Many thanks in advance. P.S May it help if I minimize a smaller system and replicate it after that. How exactly can I do replication? This message was sent using IMP, the Internet Messaging Program. -- 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_msd bug
No -it is not a typo - my cluster allows me to use higher amount of memory than 10%. Information I received from administrator of the cluster : [root@isei ~]#top top - 13:52:23 up 30 days, 3:00, 76 users, load average: 5.85, 17.19, 13.08 Tasks: 2825 total, 1 running, 2815 sleeping, 1 stopped, 7 zombie Cpu(s): 0.1%us, 0.7%sy, 0.0%ni, 97.2%id, 1.9%wa, 0.0%hi, 0.1%si, 0.0%st Mem: 527077804k total, 526482844k used, 594960k free, 8016k buffers Swap: 141596792k total, 141407504k used, 189288k free, 294092k cached PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 28381 stachura 34 19 307g 252g 1392 D2.2 97.5 202:57.50 g_msd It's all I have. Anyone has ever encountered such situation? Best wishes, Slawomir Wiadomość napisana przez chris.ne...@utoronto.ca w dniu 2011-06-27, o godz. 17:12: 600 GB of memory? I highly doubt that you have that much memory available. Are you sure that this is not a typo? Can you please post evidence that you have =600 GB of memory available? It is common for clusters to disallow an individual process from using 10% of the total memory on a head-node, which makes 600 MB more likely, in which case you can try submitting your job to a compute node. -- original message -- Hello, thank you for your reply. I have used following command : g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4. Indeed my network administrator was very unhappy about comsumed memory. Regards, Slawomir Wiadomo¶æ napisana przez Tsjerk Wassenaar w dniu 2011-06-27, o godz. 15:40: [Hide Quoted Text] Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 S³awomir Stachura stachura.slawo...@gmail.com: Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With time of calculations the memory reserves are gradually devoured to the extent, in my case, of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps in memory. Have you heard of such case? Best wishes, -- 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] minimization problem (Martini simulation)
pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I forgot to note that I'm talking about a Martini simulation. I'm trying to set up simulation. I have a big simulation of something like half million CG atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax 10 This is not really an error: http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision The success of any subsequent MD depends on the magnitude of the maximum force the EM procedure achieved. Minimizing to such a low force is very difficult and may not be possible for all systems. I tried to use a bigger emtol(emtol=20) and it still didn't converge.However I still run the MD with dt = 0.03 and nstxout = 1. after something like 100 steps the system blow up. Perhaps your EM wasn't sufficient, but based on the information you've posted, it's hard to draw any real conclusion about that. I will appreciate any help with this issue. Many thanks in advance. P.S May it help if I minimize a smaller system and replicate it after that. How exactly can I do replication? It may or may not help, but I don't think it likely. You can always try it and see. Certainly minimizing a smaller system will give you a faster result. You can replicate any unit cell in any dimension using genconf -nbox. -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] Re: gmx-users Digest, Vol 86, Issue 183
Hi Justin, I have used the same files to re-run using gromacs-4.5.4 and the only difference is that I get a segmentation fault instead of bus error message. Thanks for your help, I will then fill out the issue report as you suggested. Best, Thereza Professor Thereza A. Soares Departamento de Química Fundamental Universidade Federal de Pernambuco Av. Jornalista Anibal Fernandes, s/nº Cidade Universitária 50740-560 Recife, PE, Brazil tel: +558121268440 fax: +558121268442 thereza.soa...@ufpe.br website@dqf http://dqfnet.ufpe.br/biomat/ On Jun 27, 2011, at 12:06 PM, gmx-users-requ...@gromacs.org wrote: Date: Mon, 27 Jun 2011 10:28:46 -0300 From: Thereza Soares thereza.soa...@ufpe.br Subject: [gmx-users] Comparing MD ensembles with exp. NOE restraints -- bus error To: gmx-users@gromacs.org Message-ID: 032ec9e3-5b6e-466c-a785-3adfc44f4...@ufpe.br Content-Type: text/plain; charset=windows-1252 Hi There, I would like to compare my ensemble of (unrestrained) MD structures against experimental NOE distances. For that, I have added the distance_restraints block to my *.top file such as: [distance_restraints] ;aiaj type index type‚ low up1 up2 fac 3331101 0.0 3.000 1.2 0.4 3531111 0.0 2.500 0.7 0.3 I have also added the disre options below to the *.mdp file used to generate a new tpr for the NOE analysis disre = Simple disre-weighting = Equal disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 1 When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives a bus error ... I am copying the entire mdp file in case someone can point me out what is wrong with it. I would appreciate any suggestions on what maybe wrong here, Cheers, Thereza integrator = md dt = 0.002 nsteps = 2500 nstxout = 500 nstvout = 500 nstlog = 500 nstenergy= 500 nstxtcout= 500 comm-mode= Linear nstcomm = 5 comm-grps= SYSTEM xtc_grps = SYSTEM energygrps = SYSTEM nstlist = 5 rlist= 1.4 coulombtype = generalized-reaction-field epsilon_rf = 66.0 ns_type = grid rcoulomb = 1.4 rvdw = 1.4 pbc = xyz tcoupl = berendsen tc-grps = SYSTEM tau_t= 0.2 ref_t= 300 Pcoupl = berendsen Pcoupltype = semi-isotropic tau_p= 0.4 0.4 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 gen_vel = yes gen_temp = 10 gen_seed = 178296 constraints = h-bonds disre = simple disre-weighting = equal disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 1 -- Message: 2 Date: Mon, 27 Jun 2011 09:49:29 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Comparing MD ensembles with exp. NOE restraints -- bus error To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e088a69.7080...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed Thereza Soares wrote: Hi There, I would like to compare my ensemble of (unrestrained) MD structures against experimental NOE distances. For that, I have added the distance_restraints block to my *.top file such as: [distance_restraints] ;aiaj type index type‚ low up1 up2 fac 3331101 0.0 3.000 1.2 0.4 3531111 0.0 2.500 0.7 0.3 I have also added the disre options below to the *.mdp file used to generate a new tpr for the NOE analysis disre = Simple disre-weighting = Equal disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 1 When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives a bus error ... I am copying the entire mdp file in case someone can point me out what is wrong with it. There is nothing wrong with the .mdp file. There is likely a bug in the g_disre code somewhere, as is usually the case with immediate bus errors or segmentation faults. I would appreciate any suggestions on what maybe wrong here, You haven't mentioned which version of Gromacs you're using, but if it is not 4.5.4 (the latest), please try again with this version. If you are using 4.5.4 or the error persists, please file an issue report on redmine.gromacs.org and include your .tpr and .pdb files necessary to reproduce the problem. -Justin --
[gmx-users] g_covar : segmentation fault
Hi, I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA Below are the commands i used: 1) I generated index file for chosen dihedral angles. 2) g_angle -f 100ns_noPBC.xtc -n dangle.ndx -or dangle.trr -type dihedral 3) trjconv -s md_100ns.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0 4) g_covar -f dangle.trr -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc -s resized.gro While running the command in step 4, it runs for sometime and then i get segmentation fault. I was doing these in Gromacs 4.5.4 package. When i switched to Gromacs 4.0.7 package and repeated the steps, i ran successfully without any errors. Please can I know what changes can be done to the commands I have used so that i can get it running with Gromacs 4.5.4 package as well. Kind regards, chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt Besuchen Sie uns auf unserem neuen Webauftritt unter www.fz-juelich.de -- 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_covar : segmentation fault
Poojari, Chetan wrote: Hi, I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA Below are the commands i used: 1) I generated index file for chosen dihedral angles. 2) g_angle -f 100ns_noPBC.xtc -n dangle.ndx -or dangle.trr -type dihedral 3) trjconv -s md_100ns.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0 4) g_covar -f dangle.trr -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc -s resized.gro While running the command in step 4, it runs for sometime and then i get segmentation fault. I was doing these in Gromacs 4.5.4 package. When i switched to Gromacs 4.0.7 package and repeated the steps, i ran successfully without any errors. Please can I know what changes can be done to the commands I have used so that i can get it running with Gromacs 4.5.4 package as well. Typically, when an old version works and the new version is broken, a bug is at fault. If you consistently observe this behavior with other systems or smaller systems (to rule out simply running out of memory, etc), then please file a bug report on redmine.gromacs.org with all necessary input files to reproduce the problem. -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] The RMSD of a metal ion
Hi, I would like to look at the positions of a metal ion in MD relative to its original crystal position. I tried g_rms, and I got the following message: Fatal error : Need = 3 points to fit Did I use the correct command to achieve this task? Thanks for your insight in advance. Simon -- 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] The RMSD of a metal ion
simon sham wrote: Hi, I would like to look at the positions of a metal ion in MD relative to its original crystal position. I tried g_rms, and I got the following message: Fatal error : Need = 3 points to fit Did I use the correct command to achieve this task? Generally, when one receives a fatal error, the answer is no :) To do least-squares fitting, as the error says, three points are needed. In your case, I suspect you have chosen the metal ion as the fitting and calculation group, so there is only one point in space to which fitting can be applied. Even if g_rms ran, it would give you a zero RMSD, as fitting would always align the single ion with itself. You will have to either fit to some other suitable reference group such that the RMSD of the metal ion is calculated relative to it, or do a rotational and translational fit of the trajectory with trjconv and issue g_rms -nofit to calculate the RMSD of the metal ion. -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] minimization problem (Martini simulation)
Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying EM wasn't sufficient. What information do you need in order be able to help? I run EM with emtol=60 and I got the following energies: Steepest Descents converged to Fmax 60 in 2256 steps Potential Energy = -1.2244622e+07 Maximum force = 4.7755444e+01 on atom 1659 Norm of force = 6.3245118e-01 Everything seems ok. After that I run MD using mdp file attached and I got the following error: Started mdrun on node 0 Tue Jun 28 00:10:12 2011 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR) 6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03 Cons. rmsd () 4.25390e-06 DD step 9 load imb.: force 3.0% --- Program mdrun_mpi, VERSION 4.0.3 Source code file: nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. --- Step Aside, Butch (Pulp Fiction) I found that this error is connected to problems with minimization but unfortunately I don't know how to fix it. I will appreciate very much any help. Thank you. Regina mdp file used: ; VARIOUS PREPROCESSING OPTIONS = title= Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0.0 dt = 0.030 nsteps = 4000 ; number of steps for center of mass motion removal = nstcomm = 1 ; Groups for center of mass motion removal comm-grps= System ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = Protein_PSE W_ION ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = Protein_PSE W_ION ; Time constant (ps) and reference temperature (K) = tau_t= 1.0 1.0 ref_t= 300 300 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 5.0 5.0 compressibility = 3e-4 3e-4 ref_p= 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 300 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 Quoting Justin A. Lemkul jalem...@vt.edu: pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I forgot to note that I'm talking about a Martini simulation. I'm trying to set up simulation. I have a big simulation of something like half million CG atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax 10 This is not really an error:
Re: [gmx-users] minimization problem (Martini simulation)
pol...@fh.huji.ac.il wrote: Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying EM wasn't sufficient. What information do you need in order be able to help? I run EM with emtol=60 and I got the following energies: Steepest Descents converged to Fmax 60 in 2256 steps Potential Energy = -1.2244622e+07 Maximum force = 4.7755444e+01 on atom 1659 Norm of force = 6.3245118e-01 This was the information I wanted to see. Without it, no one had any idea if your EM converged reasonably. Everything seems ok. Indeed it does. After that I run MD using mdp file attached and I got the following error: Started mdrun on node 0 Tue Jun 28 00:10:12 2011 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR) 6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03 Here's your problem. The initial temperature is ridiculously small, indicating something has gone wrong. Cons. rmsd () 4.25390e-06 DD step 9 load imb.: force 3.0% --- Program mdrun_mpi, VERSION 4.0.3 Any reason you're using a really old version of Gromacs? snip Here's your problem. The combination of: tcoupl = Berendsen and gen_vel = no is generally not stable. You should set gen_vel = yes to start a reasonable equilibration period. -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] pull direction of steered MD in Gromacs
Dear Gromacs Users, Can you assign any pulling direction in Gromacs rather than only using the axial x/y/z direction? pull_dim= N N Y Can we assign sth. like a vector in gromacs? Thanks, Tom -- 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] pull direction of steered MD in Gromacs
Tom wrote: Dear Gromacs Users, Can you assign any pulling direction in Gromacs rather than only using the axial x/y/z direction? pull_dim= N N Y Can we assign sth. like a vector in gromacs? Yes, see the pull_vec option and other related topics in the pulling tutorial: http://www.gromacs.org/Documentation/Tutorials?highlight=tutorials#Pull_Code_and_Umbrella_Sampling -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_msd bug
On 27/06/2011 11:57 PM, Sławomir Stachura wrote: Hello, thank you for your reply. I have used following command : g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4. Indeed my network administrator was very unhappy about comsumed memory. I'd guess that using only part of your trajectory at one time (g_msd -b -e, or pre-condition with trjconv) will lead to less memory usage - although the implementation of this code should not require 600GB unless you actually have many millions of atoms. Mark Regards, Slawomir Wiadomość napisana przez Tsjerk Wassenaar w dniu 2011-06-27, o godz. 15:40: Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 Sławomir Stachurastachura.slawo...@gmail.com: Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With time of calculations the memory reserves are gradually devoured to the extent, in my case, of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps in memory. Have you heard of such case? Best wishes, Slawomir-- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] plateau in msd (glass transition); ref_t
On Jun 23, 2011, at 5:07 AM, Anja Kuhnhold wrote: I'm simulating a bead-spring polymer model (1600 chains and 10 beads per chain in a 26.6^3 box with pbc) with LJ and FENE potentials. I calculate the mean-square-displacement for different temperatures. For T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass transition)- but there is none. The curve for T=0.46 is similar to the one for T=1.0 (above glass transition) with only a small shift to lower values- but no plateau. Why did you expect a plateau at T=0.46 for this system? Is there any published literature out there for your system? Also, keep in mind that many people wouldn't call a plateau in the rmsd curve a glass transition. My .mdp-files look as follows: integrator = md-vv dt = 0.0035 nsteps = 100 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 ns_type = grid pbc = xyz periodic_molecules = yes rvdw = 1.12 rlist = 1.3 tcoupl = nose-hoover tc-grps = System tau_t = 20 ref_t = 55.32 vdwtype = Shift rcoulomb = 1.12 coulombtype = Reaction-Field-zero epsilon_rf = 0 Is the ref_t correct? That depends on the interaction energy you specified in the force field parameter file. The results in the md.log file say T is about 89. Oh, that's weird. Are you sure your system is equilibrated? Hope this helps, Lutz -- 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
