[gmx-users] Range checking error
Dear all, I am simulating a protein along with a ligand molecule. The ligand molecule is modeled as per the literature. The ligand molecule consists of FE and S alone and in addition to that it is covalently bonded with the enzyme's cys residue. So I have modeled my ligand FE4S4 with SG and CB atoms of cystine. I have included only bonded terms in my forcefield for my ligand (since I do not know other terms like angle and dihedral angles force constants etc) and the article does not mention these. Now the problem is, when I try to run energy minimization , I encounter Range checking error: and the detailed error is pasted below. So I suspect this error is due to inadequate force field data like angles and dihedrals. Or is it caused by some other factor?.But one thing I am sure of is , when I simulate my system without the ligand, the error disappears. I am unable to find any answer to this query in the forum. Kindly extend your help this time as you always do. # Steepest Descents: Tolerance (Fmax) = 2.0e+02 Number of steps= 5000 Warning: 1-4 interaction between 2446 and 2468 at distance 6.079 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step=0, Dmax= 1.0e-02 nm, Epot= nan Fmax= 1.71540e+115, atom= 2452 --- Program mdrun_d, VERSION 4.0 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 4096 ] # Thank You Jyotsna On Wed, 03 Feb 2010 22:42:09 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* - Original Message - From: 011013021-Jyotsna 011013...@bioinfo.sastra.edu Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users gmx-users@gromacs.org Dear David, Thanks for your reply. From your reply, I get the impression that the bond length of my hydrogen molecule gets adjusted duing minimization of the whole system ( protien+water+ inserted hydrogen molecule). But the issue impending is the insertion of the hydrogen molecule itself into the protein+water box created in previous step. For insertion/addition of hydrogen molecules I used the command: genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top ci h2.gro nmol 100 What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when there's no water, and then solvate *afterwards*. Or, generate solvent, and get a list of 100 random numbers in the right range, manually delete those water molecules to create interstices, update your [molecules] section, then use genconf -ci and equilibrate carefully to fix the density. Or, generate solvent for a box somewhat smaller than the one you want, use editconf -scale to scale the coordinates up to create interstices, use genconf -ci and then minimize really gently to fix all the bond lengths, and equilibrate carefully to fix the density. Mark It reports to me the inability to add any of the hydrogen molecules, ie it adds 0 molecules out of 100 requested. ###error Reading molecule configuration Gallium Rubidium Oxygen Manganese Argon Carbon Silicon Containing 3 atoms in 1 residue Initialising van der waals distances... Try 999 Added 0 molecules (out of 100 requested) of H2 Writing generated configuration to 2frv.solv.gro Back Off! I just backed up 2frv.solv.gro to ./#2frv.solv.gro.1# PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE Output configuration contains 8340 atoms in 977 residues Volume : 1299.08 (nm^3) Density : 143.043 (g/l) Number of SOL molecules: 186 Processing topology Removing line #40 'SOL 39308' from topology file (2frv.top) error end### How do i rectify this problem? I suspect the problem is due to the bond length of the hydrogen molecule that I created with 1.66A distance ( as described in my previous post) and the fact that the gap between the solvent molecules (in my case , water) is not big
Re: [gmx-users] Range checking error
011013021-Jyotsna wrote: Dear all, I am simulating a protein along with a ligand molecule. The ligand molecule is modeled as per the literature. The ligand molecule consists of FE and S alone and in addition to that it is covalently bonded with the enzyme's cys residue. So I have modeled my ligand FE4S4 with SG and CB atoms of cystine. I have included only bonded terms in my forcefield for my ligand (since I do not know other terms like angle and dihedral angles force constants etc) and the article does not mention these. Now the problem is, when I try to run energy minimization , I encounter Range checking error: and the detailed error is pasted below. So I suspect this error is due to inadequate force field data like angles and dihedrals. Or is it caused by some other factor?.But one thing I am sure More likely the underlying physics is unreasonable. See here: http://www.gromacs.org/Documentation/Errors#Range_Checking_error of is , when I simulate my system without the ligand, the error disappears. I am unable to find any answer to this query in the forum. Kindly extend your help this time as you always do. # Steepest Descents: Tolerance (Fmax) = 2.0e+02 Number of steps= 5000 Warning: 1-4 interaction between 2446 and 2468 at distance 6.079 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step=0, Dmax= 1.0e-02 nm, Epot= nan Fmax= 1.71540e+115, atom= 2452 You should have seen these errors in the list archive if you did a search. Your system is clearly blowing up (see link above). Your Fmax is essentially infinite, which is usually due to extreme atomic overlap, which should be clear in the input structure. Otherwise, mdrun is giving you clues about atoms 2446 and 2468 - start investigating there. --- Program mdrun_d, VERSION 4.0 Source code file: nsgrid.c, line: 357 I would also encourage you to upgrade to the latest version (4.0.7); it will not fix your problem, but there have certainly been some important bug fixes related to stability and usability that will make your life easier :) -Justin Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 4096 ] # Thank You Jyotsna On Wed, 03 Feb 2010 22:42:09 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* - Original Message - From: 011013021-Jyotsna 011013...@bioinfo.sastra.edu Date: Wednesday, February 3, 2010 21:48 Subject: Re: [gmx-users] H2 topology To: Discussion list for GROMACS users gmx-users@gromacs.org Dear David, Thanks for your reply. From your reply, I get the impression that the bond length of my hydrogen molecule gets adjusted duing minimization of the whole system ( protien+water+ inserted hydrogen molecule). But the issue impending is the insertion of the hydrogen molecule itself into the protein+water box created in previous step. For insertion/addition of hydrogen molecules I used the command: genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top –ci h2.gro –nmol 100 What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when there's no water, and then solvate *afterwards*. Or, generate solvent, and get a list of 100 random numbers in the right range, manually delete those water molecules to create interstices, update your [molecules] section, then use genconf -ci and equilibrate carefully to fix the density. Or, generate solvent for a box somewhat smaller than the one you want, use editconf -scale to scale the coordinates up to create interstices, use genconf -ci and then minimize really gently to fix all the bond lengths, and equilibrate carefully to fix the density. Mark It reports to me the inability to add any of the hydrogen molecules, ie it adds 0 molecules out of 100 requested. ###error Reading molecule configuration Gallium Rubidium Oxygen Manganese Argon Carbon Silicon Containing 3 atoms in 1 residue Initialising van der waals distances... Try 999 Added 0
[gmx-users] Range checking error: only on double precision
Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not using ffamber if you are running automated tests, since there are quirks with requiring specific nomenclature (for lysine, histidine, terminal residues, etc). -Justin Jack Shultz wrote: Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
I guess its the amber03 force field I'm having issues with. The lysozyme tutorial works if I use -ff G43a2 Thanks Jack On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul jalem...@vt.edu wrote: Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not using ffamber if you are running automated tests, since there are quirks with requiring specific nomenclature (for lysine, histidine, terminal residues, etc). -Justin Jack Shultz wrote: Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error
My initial input file is a model which was generated using Modeller, and it is a part of the original structure. I am considering fragments of a particular structure for my analysis. Could this be a possible problem for running a simulation?? I suppose there is a problem when I try to convert this PDB file into a .gro file. But I have no clue as to what the possible problem could be. The format of my input PDB file is correct. Also I tried to run a job for the original PDB structure which worked perfectly fine. [EMAIL PROTECTED] wrote: Dear members I happened to get an error which is as follows : Range checking error: I think it is a problem with energy minimisation and neutralising the system. However I tried many ways to solve the issue, it still seems to give me the same error. Could anyone suggest what could be the possible cause of this error. There's a problem with either your original structure, or the topology with which you're trying to describe its physics. You can find some clues here http://wiki.gromacs.org/index.php/Errors#mdrun for causes for similar problems, but without more information, we're guessing. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
[EMAIL PROTECTED] wrote: My initial input file is a model which was generated using Modeller, and it is a part of the original structure. I am considering fragments of a particular structure for my analysis. Could this be a possible problem for running a simulation?? I suppose there is a problem when I try to convert this PDB file into a .gro file. But I have no clue as to what the possible problem could be. The format of my input PDB file is correct. Well, you don't need a .gro file - see http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file Chopping something into fragments is a great way to make chemical nonsense, but pdb2gmx and grompp will often give you warnings and errors about such things. Read them carefully and pay attention! Also I tried to run a job for the original PDB structure which worked perfectly fine. Well that means your problem came with something you did... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range checking error
Dear members I happened to get an error which is as follows : Error on node 17, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 17 out of 32 gcq#106: Step Aside, Butch (Pulp Fiction) node26:19.MPID_CH_Abort: node26:19.Aborting program! node26:17.MPID_CH_Abort: node26:17.Aborting program! node26:16.MPID_CH_Abort: node26:16.Aborting program! node26:18.MPID_Abort: node26:18.MPI Abort by user Aborting program ! node26:18.MPID_CH_Abort: node26:18.Aborting program! --- Program mdrun_mpi, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 658503 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Step Aside, Butch (Pulp Fiction) Error on node 16, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 16 out of 32 gcq#106: Step Aside, Butch (Pulp Fiction) I think it is a problem with energy minimisation and neutralising the system. However I tried many ways to solve the issue, it still seems to give me the same error. Could anyone suggest what could be the possible cause of this error. Thanks in advance Sincerely Namitha ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
[EMAIL PROTECTED] wrote: Dear members I happened to get an error which is as follows : Range checking error: I think it is a problem with energy minimisation and neutralising the system. However I tried many ways to solve the issue, it still seems to give me the same error. Could anyone suggest what could be the possible cause of this error. There's a problem with either your original structure, or the topology with which you're trying to describe its physics. You can find some clues here http://wiki.gromacs.org/index.php/Errors#mdrun for causes for similar problems, but without more information, we're guessing. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range checking error
Dear gmx-users, I run MD for a protein molecule solvated with water molecules. Until now it works well, however strangely they started to crash, I don't know the reason. So, if anyone have similar problem please let me know the solution. It seems like that NPT system might cause some problems. Also, when I continue MD further, it works. (Sometimes simulation crashes after 1 ns, but sometimes it crashes only after 100 ps.) Then, can I use those results for further studies? This is the mdp file: integrator = md nsteps = 150 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 pcoupl = Berendsen pcoupltype = isotropic tau-p = 1 ref-p = 1.0 compressibility = 4.5e-5 constraints = all-bonds constraint_algorithm = lincs nstxout = 1000 nstvout = 1 nstxtcout = 100 nstenergy = 100 ; Generate velocity is on at 300 K gen_vel = yes gen_temp= 300.0 gen_seed= 173529 This is the error message: --- Program mdrun_mpi_d, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 3185. It should have been within [ 0 .. 3072 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Interfacing Space and Beyond... (P. J. Harvey) Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi_d on CPU 1 out of 16 gcq#307: Interfacing Space and Beyond... (P. J. Harvey) [1] MPI Abort by user Aborting program ! [1] Aborting program! --- -- -- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECTED] [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
SeungPyo Hong wrote: Dear gmx-users, I run MD for a protein molecule solvated with water molecules. Until now it works well, however strangely they started to crash, I don't know the reason. So, if anyone have similar problem please let me know the solution. It seems like that NPT system might cause some problems. You need to prepare your system better, and/or equilibrate more gently. See http://wiki.gromacs.org/index.php/blowing_up and links thereon. Pay attention to any warning messages from grompp. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
Yanzi Zhou wrote: Dear Gromacs-Users, Can anybody help me? When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes with double precision gromacs compiled by Intel compiler on x86_64 GNU/Linux, it was crashing at about 100 ps with a message: --- Program mdrun_mpi_d, VERSION 3.3.2 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 4421. It should have been within [ 0 .. 4212 ] --- But it can be finished when I use 1 or 2 processes, or use cut-off for electrostatics instead of PME, or for a NVT system, or with single precision gromacs. I have noticed the bug #167 on Bugzilla, and modified routine stat.c, but it did no help, and actually I didn't write to XTC file. Maybe, there are still bugs for double precision gromacs? More likely the compiler. Please retry with gcc. Thanks for any help. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
Thank you. I recompiled the software with gcc, but my job still crashed at about 170ps. I tried 1 ns simulation for 1PGB in water downloaded from http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. But when I tried to do NTP simulation of DPPC from the benchmarks of Gromacs, my job died on 6 processes with double precision gromacs. I found the job crashed when I: do NTP simulation for a large system, and use PME on more than two processors with double precision gromacs. David van der Spoel wrote: Yanzi Zhou wrote: Dear Gromacs-Users, Can anybody help me? When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes with double precision gromacs compiled by Intel compiler on x86_64 GNU/Linux, it was crashing at about 100 ps with a message: --- Program mdrun_mpi_d, VERSION 3.3.2 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 4421. It should have been within [ 0 .. 4212 ] --- But it can be finished when I use 1 or 2 processes, or use cut-off for electrostatics instead of PME, or for a NVT system, or with single precision gromacs. I have noticed the bug #167 on Bugzilla, and modified routine stat.c, but it did no help, and actually I didn't write to XTC file. Maybe, there are still bugs for double precision gromacs? More likely the compiler. Please retry with gcc. Thanks for any help. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
Yanzi Zhou wrote: Thank you. I recompiled the software with gcc, but my job still crashed at about 170ps. I tried 1 ns simulation for 1PGB in water downloaded from http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. But when I tried to do NTP simulation of DPPC from the benchmarks of Gromacs, my job died on 6 processes with double precision gromacs. I found the job crashed when I: do NTP simulation for a large system, and use PME on more than two processors with double precision gromacs. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. What have you done to check that your system preparation protocol is reasonable? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
I did MD simulation for lipid. I downloaded the pre-equilibrated structure and parameters from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I can do 5 ns NTP simulation with single precision, but it can't go on with double precision. I also tried the DPPC from the benchmarks of Gromacs. I first did the NTV simulation for 500 ps, and then do NTP simulation using PME, but crashed. Mark Abraham wrote: Yanzi Zhou wrote: Thank you. I recompiled the software with gcc, but my job still crashed at about 170ps. I tried 1 ns simulation for 1PGB in water downloaded from http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. But when I tried to do NTP simulation of DPPC from the benchmarks of Gromacs, my job died on 6 processes with double precision gromacs. I found the job crashed when I: do NTP simulation for a large system, and use PME on more than two processors with double precision gromacs. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. What have you done to check that your system preparation protocol is reasonable? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error issue
Mark Abraham wrote:
Matteo Guglielmi wrote:
I did what you suggest and even more, I decreased the timestep to 0.001
Well the problem doesn't go away.
I've been reading mails from this discussion list... I'm not the only
who's experiencing this kind of problem (ci variable range error)...
actually few gmx users suggest it comes only from parallel runs which
is my case BTW.
I've seen it most often when equilibration hasn't happened properly,
but you'd think 1.5ns would be enough to avoid a crash.
I'm running parallel runs on different clusters... it's happening
everywhere.
Do serial runs do it?
Have you looked at your trajectory visually to see where things start
going wrong?
Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
I did no try any serial run yet... trajectory looks fine... but log
files might explain
why parallel runs keep crashing.
Usually I run gromacs on a dual Xeon 5140 cpus machine (2x2-cores) in
double precision.
I did compile gromacs using the intel compilers - 9.1 series:
[EMAIL PROTECTED] ~]$ icc -V
Intel(R) C Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
[EMAIL PROTECTED] ~]$ icpc -V
Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
[EMAIL PROTECTED] ~]$ ifort -V
Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_fc_c_9.1.045
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
compilatition setup detalis ###
export F77='ifort'
export CC='icc'
export CFLAGS='-axT -unroll -ip -O3'
export FFLAGS='-axT -unroll -ip -O3'
export CPPFLAGS=-I${HOME}/Software/fftw-3.1.2/include
export LDFLAGS=-L${HOME}/Software/fftw-3.1.2/lib
./configure --enable-double --with-fft=fftw3 --program-suffix=''
--enable-fortran --enable-threads --prefix=${HOME}/Software/gromacs-3.3.1
make
make install
make distclean
./configure --enable-mpi --enable-double --with-fft=fftw3
--program-suffix='' --enable-fortran --enable-threads
--prefix=${HOME}/Software/gromacs-3.3.1
make mdrun
make install-mdrun
#
I use openMPI 1.2.1 which was compiled with the same intel compilers
I've shown before.
All my systems were pre-geometry optimized:
emtol = 70
integrator = steep
constraints = none
md0.log ###
[EMAIL PROTECTED] ~]$ cat md0.log | grep Grid
ns_type = Grid
Grid: 10 x 12 x 13 cells
md1.log ###
[EMAIL PROTECTED] ~]$ cat md1.log | grep Grid
Grid: 10 x 12 x 13 cells
Grid: 10 x 12 x 12 cells
[EMAIL PROTECTED] ~]$ tail -40 md1.log
Rel. Constraint Deviation: Maxbetween atoms RMS
Before LINCS 0.009211 7638 7640 0.001295
After LINCS 0.00 10707 10709 0.00
Rel. Constraint Deviation: Maxbetween atoms RMS
Before LINCS 0.008704 9341 9344 0.001308
After LINCS 0.00 12623 12625 0.00
Rel. Constraint Deviation: Maxbetween atoms RMS
Before LINCS 0.009517 8162 8163 0.001276
After LINCS 0.00 8355 8357 0.00
Rel. Constraint Deviation: Maxbetween atoms RMS
Before LINCS 0.009805 7638 7640 0.001325
After LINCS 0.00 10207 10210 0.00
Rel. Constraint Deviation: Maxbetween atoms RMS
Before LINCS 0.009253 12747 12750 0.001259
After LINCS 0.00 8377 8379 0.00
Grid: 10 x 12 x 12 cells
---
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 1476. It should have been within [ 0 .. 1440 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---
Ease Myself Into the Body Bag (P.J. Harvey)
#
The same holds for md2.log
Re: [gmx-users] Range checking error issue
Matteo Guglielmi wrote: Mark Abraham wrote: Matteo Guglielmi wrote: I did what you suggest and even more, I decreased the timestep to 0.001 Well the problem doesn't go away. I've been reading mails from this discussion list... I'm not the only who's experiencing this kind of problem (ci variable range error)... actually few gmx users suggest it comes only from parallel runs which is my case BTW. I've seen it most often when equilibration hasn't happened properly, but you'd think 1.5ns would be enough to avoid a crash. I'm running parallel runs on different clusters... it's happening everywhere. Do serial runs do it? Have you looked at your trajectory visually to see where things start going wrong? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php I did no try any serial run yet... trajectory looks fine... but log files might explain why parallel runs keep crashing. Usually I run gromacs on a dual Xeon 5140 cpus machine (2x2-cores) in double precision. I did compile gromacs using the intel compilers - 9.1 series: [EMAIL PROTECTED] ~]$ icc -V Intel(R) C Compiler for Intel(R) EM64T-based applications, Version 9.1Build 20070320 Package ID: l_cc_c_9.1.049 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. [EMAIL PROTECTED] ~]$ icpc -V Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version 9.1Build 20070320 Package ID: l_cc_c_9.1.049 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. [EMAIL PROTECTED] ~]$ ifort -V Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version 9.1Build 20070320 Package ID: l_fc_c_9.1.045 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. an't post? Read http://www.gromacs.org/mailing_lists/users.php try again with gcc in that case. if that gives the same behavior then please submit a bugzilla. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error issue
David van der Spoel wrote: Matteo Guglielmi wrote: Mark Abraham wrote: Matteo Guglielmi wrote: I did what you suggest and even more, I decreased the timestep to 0.001 Well the problem doesn't go away. I've been reading mails from this discussion list... I'm not the only who's experiencing this kind of problem (ci variable range error)... actually few gmx users suggest it comes only from parallel runs which is my case BTW. I've seen it most often when equilibration hasn't happened properly, but you'd think 1.5ns would be enough to avoid a crash. I'm running parallel runs on different clusters... it's happening everywhere. Do serial runs do it? Have you looked at your trajectory visually to see where things start going wrong? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php I did no try any serial run yet... trajectory looks fine... but log files might explain why parallel runs keep crashing. Usually I run gromacs on a dual Xeon 5140 cpus machine (2x2-cores) in double precision. I did compile gromacs using the intel compilers - 9.1 series: [EMAIL PROTECTED] ~]$ icc -V Intel(R) C Compiler for Intel(R) EM64T-based applications, Version 9.1Build 20070320 Package ID: l_cc_c_9.1.049 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. [EMAIL PROTECTED] ~]$ icpc -V Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version 9.1Build 20070320 Package ID: l_cc_c_9.1.049 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. [EMAIL PROTECTED] ~]$ ifort -V Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version 9.1Build 20070320 Package ID: l_fc_c_9.1.045 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. an't post? Read http://www.gromacs.org/mailing_lists/users.php try again with gcc in that case. if that gives the same behavior then please submit a bugzilla. I did post here (gmx-users-list) because the problem I'm currently experiencing with gromacs could be related to my input file set-up... anyway, you are right. What I noticed right now in my simulation is that the volume of the box shrinks. (water molecules not equilibrated) I've also noticed that among the tree coordinates, z shrinks a bit faster than x and y. From this point of view things seem to be much more clear to me i.e. since the z coordinates is shrinking, the Grid size gets updated to the new value 10x12x12 (initial value was 10x12x13!!!). This might lead to the Range checking error if this situation is not handled properly by the gmx code. MG. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error issue
From this point of view things seem to be much more clear to me i.e. since the z coordinates is shrinking, the Grid size gets updated to the new value 10x12x12 (initial value was 10x12x13!!!). This might lead to the Range checking error if this situation is not handled properly by the gmx code. MG. As I said before, retry with gcc. Compilers suck big time, they have a billion times more bugs than gromacs. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error issue
David van der Spoel wrote: Matteo Guglielmi wrote: Hello world, the following is my input file: title= 2masn cpp = /usr/bin/cpp define = -DPOSRES integrator = md tinit= 0 dt = 0.002 nsteps = 150 init_step= 0 comm_mode= Angular nstcomm = 1 comm_grps= Pore nstxout = 25 nstvout = 25 nstfout = 25 nstcheckpoint= 1000 nstlog = 2500 nstxtcout= 2500 xtc_grps = System energygrps = Pore Membrane Ions Water nstenergy= 2500 nstlist = 5 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.4 fourier_nx = 88 fourier_ny = 88 fourier_nz = 88 pme_order= 4 ewald_rtol = 1e-5 ewald_geometry = 3d optimize_fft = yes tcoupl = berendsen tc_grps = Solute Solvent tau_t= 0.10.4 ref_t= 300300 pcoupl = berendsen pcoupltype = anisotropic tau_p= 0.5 0.5 0.5 0.50.50.5 compressibility = 4.53e-5 4.53e-5 4.53e-5 0.00.00.0 ref_p= 1.0251.0251.0251.025 1.025 1.025 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = lincs unconstrained_start = no lincs_order = 4 lincs_iter = 2 lincs_warnangle = 30 and way after the very beginning of this simulation (~1.5ns) I always get this error message: ## Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.032676 17797 17799 0.003970 After LINCS 0.04 17162 17169 0.00 Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells --- Program mdrun_mpi, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1434. It should have been within [ 0 .. 1320 ] Please report this to the mailing list (gmx-users@gromacs.org) --- # Is my input file so bad? I would increase tau_p to at least 5 ps for anisotropic coupling. (I've seen people using lincs with 5fs time step...) Thanks for any useful suggestion, MG. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php I did what you suggest and even more, I decreased the timestep to 0.001 Well the problem doesn't go away. I've been reading mails from this discussion list... I'm not the only who's experiencing this kind of problem (ci variable range error)... actually few gmx users suggest it comes only from parallel runs which is my case BTW. I'm running parallel runs on different clusters... it's happening everywhere. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error issue
Matteo Guglielmi wrote: I did what you suggest and even more, I decreased the timestep to 0.001 Well the problem doesn't go away. I've been reading mails from this discussion list... I'm not the only who's experiencing this kind of problem (ci variable range error)... actually few gmx users suggest it comes only from parallel runs which is my case BTW. I've seen it most often when equilibration hasn't happened properly, but you'd think 1.5ns would be enough to avoid a crash. I'm running parallel runs on different clusters... it's happening everywhere. Do serial runs do it? Have you looked at your trajectory visually to see where things start going wrong? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error issue
Matteo Guglielmi wrote: Hello world, the following is my input file: title= 2masn cpp = /usr/bin/cpp define = -DPOSRES integrator = md tinit= 0 dt = 0.002 nsteps = 150 init_step= 0 comm_mode= Angular nstcomm = 1 comm_grps= Pore nstxout = 25 nstvout = 25 nstfout = 25 nstcheckpoint= 1000 nstlog = 2500 nstxtcout= 2500 xtc_grps = System energygrps = Pore Membrane Ions Water nstenergy= 2500 nstlist = 5 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.4 fourier_nx = 88 fourier_ny = 88 fourier_nz = 88 pme_order= 4 ewald_rtol = 1e-5 ewald_geometry = 3d optimize_fft = yes tcoupl = berendsen tc_grps = Solute Solvent tau_t= 0.10.4 ref_t= 300300 pcoupl = berendsen pcoupltype = anisotropic tau_p= 0.5 0.5 0.5 0.50.50.5 compressibility = 4.53e-5 4.53e-5 4.53e-5 0.00.00.0 ref_p= 1.0251.0251.0251.025 1.025 1.025 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = lincs unconstrained_start = no lincs_order = 4 lincs_iter = 2 lincs_warnangle = 30 and way after the very beginning of this simulation (~1.5ns) I always get this error message: ## Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.032676 17797 17799 0.003970 After LINCS 0.04 17162 17169 0.00 Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells Grid: 10 x 12 x 12 cells Grid: 10 x 11 x 12 cells --- Program mdrun_mpi, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1434. It should have been within [ 0 .. 1320 ] Please report this to the mailing list (gmx-users@gromacs.org) --- # Is my input file so bad? I would increase tau_p to at least 5 ps for anisotropic coupling. (I've seen people using lincs with 5fs time step...) Thanks for any useful suggestion, MG. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] range checking error
Dear Users, I am running MD of an homology model and even with a long energy minimization step a still get this error message: Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 1200 ] Please report this to the mailing list (gmx-users@gromacs.org) Thanks in advance, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] range checking error
Hi Giacomo, That is due to the bad starting structure. You might want to try with small time step and with no constrain. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Giacomo Bastianelli Sent: Tue 05/12/2006 10:16 AM To: Discussion list for GROMACS users Subject: [gmx-users] range checking error Dear Users, I am running MD of an homology model and even with a long energy minimization step a still get this error message: Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 1200 ] Please report this to the mailing list (gmx-users@gromacs.org) Thanks in advance, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range checking error: ci barely out of bounds.
I am attempting to solve my range checking errors where ci is just barely out of bounds. This particular run is on 4cpus. I have reposted because now I have noticed that a0.log differs from the other log files with respect to the reported cells in the grid and that this may be important. Any help is greatly appreciated. My error message is: Variable ci has value 1625. It should have been within [ 0 .. 1584 ] And I notice that 12 x 12 x 11 = 1584, but 13 x 12 x 11 = 1716 (which would put ci=1625 in bounds). grep 'Grid:' a0.log | wc -l = 24 lines grep 'Grid:' (a1.log or a2.log or a3.log) | wc -l = 25 lines The straight grep 'Grid:' output is: ... Grid: 12 x 12 x 11 cells Grid: 13 x 12 x 11 cells (a0.log does not contain this line) The same pattern tends to occur for different jobs. For another example, Grid: 13 x 13 x 10 cells -- Grid: 13 x 13 x 11 cells (not on a0.log) and ci = 1721. It should have been within [ 0 .. 1690 ] (But 13 x 13 x 11 = 1859 putting 1721 in bounds). Can the grid sizes be different for the different processors or is this an output artifact? Here is my MDP file: title = seriousMD cpp = /home/cneale/exe/cpp integrator = md nsteps = 35 tinit = 0 dt = 0.002 comm_mode = linear nstcomm = 1 comm_grps = System nstxout = 5 nstvout = 5 nstfout = 5 nstlog = 1000 nstlist = 10 nstenergy = 5000 nstxtcout = 5000 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= no Pcoupl = Berendsen pcoupltype = semiisotropic compressibility = 4.5e-5 4.5e-5 ref_p = 1. 1. tau_p = 4.04.0 tcoupl = Berendsen tc_grps = Protein LDA_POPE_DMPE SOL_NA+ tau_t = 0.1 0.1 0.1 ref_t = 300.300. 300. annealing = no gen_vel = yes unconstrained-start = no gen_temp= 300. gen_seed= 9896 constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 4 There is more background information and run data here: http://www.gromacs.org/pipermail/gmx-users/2006-October/024154.html http://www.gromacs.org/pipermail/gmx-users/2006-September/024003.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range checking error: ci barely out of bounds.
Hello, I previously posted a problem about crashes in parallel but not serial: http://www.gromacs.org/pipermail/gmx-users/2006-September/024003.html I resolved that problem by running 5ns in serial and then, once I no longer needed to restrain the crystal waters, adding them to the main TIP4P SOL group. I then moved my unrestrained simulation to 4cpu parallel and everything went fine for 1.5ns when it crashed (see bottom for text output upon crash). The energy is stable when viewing output from each 2ps. So is the pressure based on the .edr and viewing the .xtc, both saved every 10ps. Total Energy: -8e5 +/- 450 Temperature: 300 +/- 1 Pressure(bar): -2 +/- 116 X(nm): 9.2 +/-0.01 Y(nm): 9.1 +/-0.01 Z(nm): 7.7 +/-0.02 This is a protein in a fully solvated membrane with 57K atoms. I am running gromacs-3.3.1 in 800ps segments usgin tpbconv -extend to set up new runs. I am using shuffle/sort and when I deshuffle the trajectory it looks good for the 1.5ns that I have. tau_p=4.0 for semiisotropic XY-Z and tau_t=0.1 for each of 3 groups. Constraints are all-bonds with lincs and dt=0.002. It may or may not be relevant that I have a double [ pairs ] list for my lipids. I have seen people post similar neighboursearching issues and received suggestions regarding pressure coupling. However, I do not see any obvious pressure issues and I am going on strong-but-not-entirely-proven evidence that this is a parallel-specific problem. Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 4.66383e+041.42350e+041.46400e+041.47575e+032.35022e+04 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coul. recip. 7.84954e+031.04413e+04 -9.08592e+03 -6.09933e+05 -4.18189e+05 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -9.18426e+051.19106e+05 -7.99320e+052.99675e+022.07330e+02 Grid: 13 x 13 x 10 cells Grid: 13 x 13 x 11 cells Grid: 13 x 13 x 10 cells Step Time Lambda 696000 1392.00.0 --- Program mdrun_mpi, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1721. It should have been within [ 0 .. 1690 ] Please report this to the mailing list (gmx-users@gromacs.org) --- 'Nay. We are but men.' Rock! (Tenacious D) # Is it significant that ci was 1721, which is much closer to [ 0 .. 1690 ] than the -82745956412 type numbers that I get when my system is exploding? Many thanks, Chris Neale. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range Checking error
Gaurav Chopra wrote: / Hi // // I am doing a steepest descent for the initial mdrun for a peptide and it // gives me the following error. Please advice. // // Thanks // Gaurav // --- // Program mdrun, VERSION 3.3 // Source code file: nsgrid.c, line: 226 // // Range checking error: // Explanation: During neighborsearching, we assign each particle to a grid // based on its coordinates. If your system contains collisions or parameter // errors that give particles very high velocities you might end up with some // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot // put these on a grid, so this is usually where we detect those errors. // Make sure your system is properly energy-minimized and that the potential // energy seems reasonable before trying again. /Please follow the advice in the above two sentences. Check your structure. I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 24594 Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006 Removing pbc first time Done rmpbc Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Grid: 10 x 10 x 20 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained I get the following Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00 bonds that rotated more than 30 degrees: also segmentation fault. Is there a different method to do energy minimization better as suggested in the range check error warning. Thanks Gaurav / // Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] // Please report this to the mailing list (gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users) // --- // // ___ // gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users // http://www.gromacs.org/mailman/listinfo/gmx-users // Please don't post (un)subscribe requests to the list. Use the www // interface or send it to gmx-users-request at gromacs.org. http://www.gromacs.org/mailman/listinfo/gmx-users // Can't post? Read http://www.gromacs.org/mailing_lists/users.php / -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se http://www.gromacs.org/mailman/listinfo/gmx-users spoel at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range Checking Error
//
// Range checking error:
// Explanation: During neighborsearching, we assign each particle to a grid
// based on its coordinates. If your system contains collisions or parameter
// errors that give particles very high velocities you might end up with some
// coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
// put these on a grid, so this is usually where we detect those errors.
// Make sure your system is properly energy-minimized and that the potential
// energy seems reasonable before trying again.
/Please follow the advice in the above two sentences. Check your structure.
I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
I get the following
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00
bonds that rotated more than 30 degrees:
turn off the constraints
Hi David
I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.
Thanks
Gaurav
---
Input Parameters:
integrator = md
nsteps = 1000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 1
nstxout = 0
nstvout = 250
nstfout = 0
nstenergy = 250
nstxtcout = 250
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 42
nky = 42
nkz = 84
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = TRUE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 20
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
andersen_seed = 815131
rlist = 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 51456
ref_t: 300
tau_t: 1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
CPU= 0, lastcg= 8223, targetcg= 4112, myshift= 0
nsb-shift = 1, nsb-bshift= 0
Neighbor Search Blocks
nsb-nodeid: 0
nsb-nnodes: 1
nsb-cgtotal: 8224
nsb-natoms: 24594
nsb-shift: 1
nsb-bshift: 0
Nodeid index homenr cgload workload
0 0 24594 8224 8224
Max number of graph edges per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.320163 nm
[gmx-users] Range Checking Error
/ //
// // Range checking error:
// // Explanation: During neighborsearching, we assign each particle to a grid
// // based on its coordinates. If your system contains collisions or
parameter
// // errors that give particles very high velocities you might end up with
some
// // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
// // put these on a grid, so this is usually where we detect those errors.
// // Make sure your system is properly energy-minimized and that the
potential
// // energy seems reasonable before trying again.
// /Please follow the advice in the above two sentences. Check your structure.
//
// I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
// and steep using -DFLEXIBLE in my mdp file and I was able to compute using
mdrun but I got the following in my log file
//
// Initiating Steepest Descents
// Center of mass motion removal mode is Linear
// We have the following groups for center of mass motion removal:
// 0: rest, initial mass: 24594
// Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
// Removing pbc first time
// Done rmpbc
// Steepest Descents:
//Tolerance (Fmax) = 1.0e+01
//Number of steps=1
// Grid: 10 x 10 x 20 cells
// Configuring nonbonded kernels...
// Testing AMD 3DNow support... not present.
// Testing ia32 SSE support... present.
//
//
// Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
// I get the following
//
// Step 0, time 0 (ps) LINCS WARNING
// relative constraint deviation after LINCS:
// max 1391229833052160.00 (between atoms 655 and 657) rms
40665803128832.00
// bonds that rotated more than 30 degrees:
/
turn off the constraints
Hi David
I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.
Thanks
Gaurav
---
Input Parameters:
integrator = md
nsteps = 1000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 1
nstxout = 0
nstvout = 250
nstfout = 0
nstenergy= 250
nstxtcout= 250
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 42
nky = 42
nkz = 84
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= TRUE
bShakeSOR= FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p= 20
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
andersen_seed= 815131
rlist= 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau= 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 1e-04
lincs_order =
Re: [gmx-users] Range Checking Error
Gaurav Chopra wrote: Gaurav Chopra wrote: / Hi // // I am doing a steepest descent for the initial mdrun for a peptide and it // gives me the following error. Please advice. // // Thanks // Gaurav // --- // Program mdrun, VERSION 3.3 // Source code file: nsgrid.c, line: 226 // // Range checking error: // Explanation: During neighborsearching, we assign each particle to a grid // based on its coordinates. If your system contains collisions or parameter // errors that give particles very high velocities you might end up with some // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot // put these on a grid, so this is usually where we detect those errors. // Make sure your system is properly energy-minimized and that the potential // energy seems reasonable before trying again. /Please follow the advice in the above two sentences. Check your structure. I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 24594 Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006 Removing pbc first time Done rmpbc Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Grid: 10 x 10 x 20 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained I get the following Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00 bonds that rotated more than 30 degrees: turn off the constraints also segmentation fault. Is there a different method to do energy minimization better as suggested in the range check error warning. Thanks Gaurav / // Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] // Please report this to the mailing list (gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users) // --- // // ___ // gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users // http://www.gromacs.org/mailman/listinfo/gmx-users // Please don't post (un)subscribe requests to the list. Use the www // interface or send it to gmx-users-request at gromacs.org. http://www.gromacs.org/mailman/listinfo/gmx-users // Can't post? Read http://www.gromacs.org/mailing_lists/users.php / -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se http://www.gromacs.org/mailman/listinfo/gmx-users spoel at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
Gaurav Chopra wrote: Hi I am doing a steepest descent for the initial mdrun for a peptide and it gives me the following error. Please advice. Thanks Gaurav --- Program mdrun, VERSION 3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Please follow the advice in the above two sentences. Check your structure. Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] Please report this to the mailing list (gmx-users@gromacs.org) --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
