Re: [gmx-users] segmentation fault on gromacs 4.5.5 after mdrun
On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote: Hello evryone, I doing a simulation of a ligand-protein interaction with gromacs 4.5.5. Everything looks fine after I equilibrate the protein-ligand complex. I'm running these commands: grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr mdrun -deffnm nvt Nevertheless, I got this error: Reading file nvt.tpr, VERSION 4.5.5 (double precision) Segmentation fault What should I do? Instantaneous failure typically indicates that the forces are nonsensically high and the constraint algorithm immediately fails. Likely the previous energy minimization did not adequately complete. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] segmentation fault on gromacs 4.5.5 after mdrun
Hello evryone, I doing a simulation of a ligand-protein interaction with gromacs 4.5.5. Everything looks fine after I equilibrate the protein-ligand complex. I'm running these commands: grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr mdrun -deffnm nvt Nevertheless, I got this error: Reading file nvt.tpr, VERSION 4.5.5 (double precision) Segmentation fault What should I do? Carlos Javier Alméciga Díaz, QF., PhD. Profesor Asistente Pontificia Universidad Javeriana Facultad de Ciencias Instituto de Errores Innatos del Metabolismo Tel: 57-1-3208320 Ext 4140-4099 Fax: 57-1-3208320 Ext 4099 Bogotá. D.C. - COLOMBIA cjalmec...@javeriana.edu.co http://www.javeriana.edu.co/ieim AVISO LEGAL: El presente correo electronico no representa la opinion o el consentimiento oficial de la PONTIFICIA UNIVERSIDAD JAVERIANA. Este mensaje es confidencial y puede contener informacion privilegiada la cual no puede ser usada ni divulgada a personas distintas de su destinatario. Esta prohibida la retencion, grabacion, utilizacion, aprovechamiento o divulgacion con cualquier proposito. Si por error recibe este mensaje, por favor destruya su contenido y avise a su remitente. En este aviso legal se omiten intencionalmente las tildes. Este mensaje ha sido revisado por un sistema antivirus, por lo que su contenido esta libre de virus. This e-mail has been scanned by an antivirus system, so its contents is virus free. -- 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] segmentation fault on g_protonate
Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-afc6131 follows. I could add them by any other ways, but g_protonate seems the right way to do. Can you help me to use g_protonate? Program received signal SIGSEGV, Segmentation fault. 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 392if (ab[i][j].oname == NULL ab[i][j].tp 0) (gdb) bt #0 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 #1 0x77b22cd7 in add_h_low (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bCheckMissing=0, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:540 #2 0x77b23b66 in add_h (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bAllowMissing=1, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:781 #3 0x77b24080 in protonate (atomsptr=0x7fffceb8, xptr=0x7fffced8, protdata=0x7fffdf30) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:894 #4 0x004020ff in cmain (argc=1, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/g_protonate.c:195 #5 0x0040224c in main (argc=5, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/main.c:29 abraços, Pedro Lacerda -- 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] segmentation fault on g_protonate
On 8/9/13 2:35 PM, Pedro Lacerda wrote: Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-afc6131 follows. I could add them by any other ways, but g_protonate seems the right way to do. Can you help me to use g_protonate? Program received signal SIGSEGV, Segmentation fault. 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 392if (ab[i][j].oname == NULL ab[i][j].tp 0) (gdb) bt #0 0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 #1 0x77b22cd7 in add_h_low (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bCheckMissing=0, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:540 #2 0x77b23b66 in add_h (pdbaptr=0x7fffc1e8, xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bAllowMissing=1, nabptr=0x7fffdf40, abptr=0x7fffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:781 #3 0x77b24080 in protonate (atomsptr=0x7fffceb8, xptr=0x7fffced8, protdata=0x7fffdf30) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:894 #4 0x004020ff in cmain (argc=1, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/g_protonate.c:195 #5 0x0040224c in main (argc=5, argv=0x7fffe0d8) at /home/peu/Downloads/gromacs/src/kernel/main.c:29 Please file a bug report on redmine.gromacs.org. g_protonate has been in varying states of disrepair for years. I hacked a fix a long time ago, but apparently something has broken again. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Segmentation fault (core dumped)
Dear all I want to study the diffusion coeffcient of CO in water. I have done the energy minimization step and got the problem segmentation fault during Equilibration. I am confused whether my input file has got some error or the error is in the processing machine.I have made the following .mdp file ; ;PREPROCESSING parameters cpp = /lib/cpp define = -DFLEX_SPCE integrator = md dt =.002 nsteps = 2500 nstcomm = 1 ;OUPUT CONTROL parameters. nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 energygrps = system ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns_type = grid rlist = 1.0 ;ELECTROSTATIC and VdW parameters. rcoulomb= 1.0 rvdw= 1.0 epsilon-r = 1 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = berendsen tc-grps = system tau_t = 0.01 ref_t = 300 ;PRESSURE COUPLING is on Pcoupl = berendsen tau_p = 0.1 compressibility = 4.6e-5 ref_p = 1.0 ;SIMULATED ANNEALING parameters are not specified. ;GENERATE VELOCITIES is on at 300 K. gen_vel = yes; ; generate initially gen_temp= 300 gen_seed= 173259 ;give different values for different trials. ;BONDS parameters pbc = xyz ; 3-D PBC constraints = all-bonds constraint-algorithm = shake unconstrained-start = no The box size is 2.1 nm. I got no information then Segmentation default.It says nothing regarding the input . I will be pleased if you provide me some suggestions. Ishwor Poudyal TU Nepal -- 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] Segmentation fault (core dumped)
On 6/6/13 4:45 AM, Ishwor Poudyal wrote: Dear all I want to study the diffusion coeffcient of CO in water. I have done the energy minimization step and got the problem segmentation fault during Equilibration. I am confused whether my input file has got some error or the error is in the processing machine.I have made the following .mdp file ; ;PREPROCESSING parameters cpp = /lib/cpp define = -DFLEX_SPCE Here's the first suspect. The water models in Gromacs were intended to be rigid. Flexibility should only be used during EM, and only if necessary to improve the outcome. Running MD with flexible water is not advised. integrator = md dt =.002 nsteps = 2500 nstcomm = 1 ;OUPUT CONTROL parameters. nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 energygrps = system ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns_type = grid rlist = 1.0 ;ELECTROSTATIC and VdW parameters. rcoulomb= 1.0 rvdw= 1.0 epsilon-r = 1 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = berendsen tc-grps = system tau_t = 0.01 This is a very restrictive value of tau_t. Normally something like 0.1 or 0.5 is more appropriate. ref_t = 300 ;PRESSURE COUPLING is on Pcoupl = berendsen tau_p = 0.1 Again, very restrictive, especially for pressure. Try 1.0 or 2.0 instead. compressibility = 4.6e-5 ref_p = 1.0 ;SIMULATED ANNEALING parameters are not specified. ;GENERATE VELOCITIES is on at 300 K. gen_vel = yes; ; generate initially gen_temp= 300 gen_seed= 173259 ;give different values for different trials. ;BONDS parameters pbc = xyz ; 3-D PBC constraints = all-bonds constraint-algorithm = shake unconstrained-start = no The box size is 2.1 nm. You're playing with fire here - if the box deviates just a little bit due to pressure oscillations, your 1.0 nm will begin to double-count interactions and violate the minimum image convention. In that case, your trajectory is junk. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] segmentation fault
Sir, I am doing membrane protein dynamics in lipid bilayer, using oplsaa force field. When I am doing minimization after genion I getting message like this Back Off! I just backed up ions_1.tpr.trr to ./#ions_1.tpr.trr.2# ack Off! I just backed up ions_1.tpr.edr to ./#ions_1.tpr.edr.2# Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Segmentation fault Why this coming?I also tried mdrun -nt 1 -deffnm ions.Is it due to any installation problem?I installed gromacs simply from the Ubuntu software center.I searched in mailing list also. Thanks 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
[gmx-users] segmentation fault
Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 485 and 490 at distance 3.874 which is larger than the 1-4 table size 2.200 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 Segmentation fault why this fault?plz give a solution to overcome it. -- 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] segmentation fault
On 11/29/12 10:44 AM, Shine A wrote: Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 485 and 490 at distance 3.874 which is larger than the 1-4 table size 2.200 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 Segmentation fault why this fault?plz give a solution to overcome it. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault while calculating water mediated H-bond with g_hbond
Hello all, I was trying to calculate solvent mediated H-bond between a amino acid residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after creating separate index) with the help of g_hbond version 4.5.3. But I am getting segmentation fault while running g_hbond. Moreover I am getting error only for this particular residue, whereas with other residues the samilar calculation is working fine. I have used the following command for the calculation: g_hbond -f traj.xtc -s md.tpr -num hbnum.xvg -hbn hbond.ndx -g hbond.log -dist hbdist.xvg -hbm hbmap.xvg -n index.ndx Please provide your suggestions to rectify the error. -- --- *Thanks and Regards,* Bipin Singh -- 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] Segmentation fault while calculating water mediated H-bond with g_hbond
There were a few bugfixes done to g_hbond since 4.5.3. Try a more recent version. Erik 23 okt 2012 kl. 17.41 skrev bipin singh: Hello all, I was trying to calculate solvent mediated H-bond between a amino acid residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after creating separate index) with the help of g_hbond version 4.5.3. But I am getting segmentation fault while running g_hbond. Moreover I am getting error only for this particular residue, whereas with other residues the samilar calculation is working fine. I have used the following command for the calculation: g_hbond -f traj.xtc -s md.tpr -num hbnum.xvg -hbn hbond.ndx -g hbond.log -dist hbdist.xvg -hbm hbmap.xvg -n index.ndx Please provide your suggestions to rectify the error. -- --- *Thanks and Regards,* Bipin Singh -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Segmentation fault, mdrun_mpi
So I have spent the past few weeks debugging my equilibration protocols, which were an odd hybrid of examples ranging from GROMACS 3.3 up to GROMACS 4.5. I have cleaned out old code. I added an in vacuo energy minimization step for the protein without solvent, and a missing NVT step after solvent is defined. I have dimly grasped that, as long as you don't require compatibility with an older simulation, the V-rescale thermostat is the current recommended choice, and that switching thermostats (unlike barostats) can cause instabilities. I now know how to examine and graph macroscopic system parameters to assess stability. I think that everything should be looking good right now -- except that it isn't, not quite. When I finally start the production MD runs, I have received two segmentation faults on two different test structures. They take a LONG time to appear -- over 1,070,000 iterations on one run, and over 2,360,000 iterations on another. On top of that, I'm not getting my usual error messages -- PME errors, or SETTLE errors. I'm not getting a dump of the last frame of my simulation. I had enough trouble accepting that my simulation parameters were set up incorrectly when I had failures 100,000 steps after starting the production MD run. Am I really supposed to believe that I still have instability problems? Here is the terminal output from one run (executing mdrun_mpi): Reading file test-prep.tpr, VERSION 4.5.4 (single precision) Making 1D domain decomposition 5 x 1 x 1 starting mdrun 'Protein t= 0.0 in water' 250 steps, 5000.0 ps. [john-linux:09596] *** Process received signal *** [john-linux:09596] Signal: Segmentation fault (11) [john-linux:09596] Signal code: Address not mapped (1) [john-linux:09596] Failing at address: 0x3e950840 [john-linux:09596] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10060) [0x7f8a8ad5c060] [john-linux:09596] [ 1] /usr/lib/libgmx_mpi.openmpi.so.6(+0x1f9670) [0x7f8a8b413670] [john-linux:09596] *** End of error message *** -- mpirun noticed that process rank 2 with PID 9596 on node john-linux exited on signal 11 (Segmentation fault). -- The .log file does NOT contain any error messages, indicating any instability. The last entry in the log file is a long chain of energy status report blocks. Here's the last one: DD step 1078799 load imb.: force 1.8% Step Time Lambda 1078800 2157.60.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.07623e+038.42439e+026.03967e+02 -2.12322e+021.95589e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 8.12766e+04 -9.12661e+02 -5.96406e+05 -4.40546e+04 -5.37227e+05 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 9.76293e+04 -4.39598e+053.10969e+02 -7.72781e+013.95185e+01 Constr. rmsd 1.90839e-05 I'm not a low-level programmer, and so I don't have to deal with this much, but... a segmentation fault generally indicates that a program is trying to write outside of its allocated memory block. The third line of the error message sent to the shell would seem to indicate exactly that. That doesn't actually sound like it has anything to do with my simulation being unstable. (However, with applications written in C, I'm willing to believe anything.) I did check on my memory usage. I have 8 GB of RAM on my system, running Ubuntu Linux 11.10, AMD 64-bit. At most, I'm using a bit more than half of my RAM (I have other, undemanding applications open besides my GROMACS terminal windows, and I also reserved one CPU core to run those apps). I think that I should be fine. If they would help, I can repost my cleaned-up MDP files. I can post graphs of potential, pressure, temperature, density, etc., from any phase in my protocol. Or you could just take my word for it that all of these parameters converge nicely during my equilibration procedure, and then remain stable throughout the production MD run. My target temperature is 310 K (37 C), and I get very close to that value on average. My average pressure and density readings are both a bit lower than my targets (0.80 bar and 988 kg/m^3, respectively), but they are consistent. I have examined a series of snapshots of my protein. It isn't undergoing any radical movements. My systems are on the small side, under 50,000 atoms. It's all amino acids and water molecules. Puzzled once again. Thanks for your advice! -- View this message in context: http://gromacs.5086.n6.nabble.com/Segmentation-fault-mdrun-mpi-tp5001601.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please
RE: [gmx-users] Segmentation fault (core dumped error)
Thanks very much for much for your help. The Carbon naotube issue is solved. I still have to figure out the polymers. Thanks for the info Regards Elie Date: Fri, 14 Sep 2012 10:31:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Segmentation fault (core dumped error) On 9/14/12 12:19 AM, Elie M wrote: Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files of CNTs and graphene (using x2top), i have found on the internet scripts (by Andrea Minoia I guess). These constitute of adding .nt2, .rtp. and .itp files to the /Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and tried to execute x2top and I got the error: ..Entries in elements.dat: 218Looking whether force field files existOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name to type translationsGenerating bonds from distances...Segmentation fault (core dumped) Can anyone please tell me the source of this error and how to fix it? x2top is telling you it found nothing in the .n2t file. Either the contents are nonexistent, formatted incorrectly, or you have a line ending issue (common with Windows OS - use dos2unix if necessary). (2) I will definitely need a top file for the polymers I will also be solvating. But I also have problems because the pdb file contains a LIG residue unrecognizable by Gromacs. I have asked this question before and I was advised to change some files accordingly but to be honest I am not really professional in that; I have asked someone who had a problem in the past but he did not know all the details because he ended up not using the modified force fields after all. Can anyone give me in details how to incorporate the residue LIG within the force field or let me know whom I can consult...A part of the pdb file with the residue LIG is: COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.1HETATM1 C LIG 1 1.481 -1.276 -0.621 1.00 0.00 CHETATM2 C LIG 1 2.216 -2.370 -1.040 1.00 0.00 CHETATM3 S LIG 1 3.770 -2.409 -0.306 1.00 0.00 SHETATM 4 C LIG 1 3.456 -0.998 0.609 1.00 0.00 CHETATM 5 C LIG 1 2.207 -0.479 0.313 1.00 0.00 CHETATM6 C LIG 1 5.156 0.676 1.386 1.00 0.00 CHETATM7 C LIG 1 4.423 -0.491 1.600 1.00 0.00 CHETATM8 C LIG 1 4.550 -1.119 2.847 1.00 0.00 CHETATM9 C LIG 1 5.256 -0.503 3.905 1.00 0.00 CHETATM 10 C LIG 1 6.107 0.592 3.667 1.00 0.00 CHETATM 11 C LIG 1 6.008 1.181 2.393 1.00 0.00 CHETATM 12 S LIG 1 7.457 2.548 5.198 1.00 0.00 ! SHETA TM 13 C LIG 1 7.220 0.945 4.621 1.00 0.00... You need to introduce some sensible set of parameters for it. Using a generic LIG for a polymer is unlikely to work. Consult the following: http://www.gromacs.org/Documentation/How-tos/Polymers http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Segmentation fault (core dumped error)
On 9/14/12 12:19 AM, Elie M wrote: Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files of CNTs and graphene (using x2top), i have found on the internet scripts (by Andrea Minoia I guess). These constitute of adding .nt2, .rtp. and .itp files to the /Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and tried to execute x2top and I got the error: ..Entries in elements.dat: 218Looking whether force field files existOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name to type translationsGenerating bonds from distances...Segmentation fault (core dumped) Can anyone please tell me the source of this error and how to fix it? x2top is telling you it found nothing in the .n2t file. Either the contents are nonexistent, formatted incorrectly, or you have a line ending issue (common with Windows OS - use dos2unix if necessary). (2) I will definitely need a top file for the polymers I will also be solvating. But I also have problems because the pdb file contains a LIG residue unrecognizable by Gromacs. I have asked this question before and I was advised to change some files accordingly but to be honest I am not really professional in that; I have asked someone who had a problem in the past but he did not know all the details because he ended up not using the modified force fields after all. Can anyone give me in details how to incorporate the residue LIG within the force field or let me know whom I can consult...A part of the pdb file with the residue LIG is: COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.1HETATM1 C LIG 1 1.481 -1.276 -0.621 1.00 0.00 CHETATM2 C LIG 1 2.216 -2.370 -1.040 1.00 0.00 CHETATM3 S LIG 1 3.770 -2.409 -0.306 1.00 0.00 SHETATM4 C LIG 1 3.456 -0.998 0.609 1.00 0.00 CHETATM5 C LIG 1 2.207 -0.479 0.313 1.00 0.00 CHETATM6 C LIG 1 5.156 0.676 1.386 1.00 0.00 CHETATM7 C LIG 1 4.423 -0.491 1.600 1.00 0.00 CHETATM8 C LIG 1 4.550 -1.119 2.847 1.00 0.00 CHETATM9 C LIG 1 5.256 -0.503 3.905 1.00 0.00 CHETATM 10 C LIG 1 6.107 0.592 3.667 1.00 0.00 CHETATM 11 C LIG 1 6.008 1.181 2.393 1.00 0.00 CHETATM 12 S LIG 1 7.457 2.548 5.198 1.00 0.00 ! SHETA TM 13 C LIG 1 7.220 0.945 4.621 1.00 0.00... You need to introduce some sensible set of parameters for it. Using a generic LIG for a polymer is unlikely to work. Consult the following: http://www.gromacs.org/Documentation/How-tos/Polymers http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault (core dumped error)
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files of CNTs and graphene (using x2top), i have found on the internet scripts (by Andrea Minoia I guess). These constitute of adding .nt2, .rtp. and .itp files to the /Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and tried to execute x2top and I got the error: ..Entries in elements.dat: 218Looking whether force field files existOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name to type translationsGenerating bonds from distances...Segmentation fault (core dumped) Can anyone please tell me the source of this error and how to fix it? (2) I will definitely need a top file for the polymers I will also be solvating. But I also have problems because the pdb file contains a LIG residue unrecognizable by Gromacs. I have asked this question before and I was advised to change some files accordingly but to be honest I am not really professional in that; I have asked someone who had a problem in the past but he did not know all the details because he ended up not using the modified force fields after all. Can anyone give me in details how to incorporate the residue LIG within the force field or let me know whom I can consult...A part of the pdb file with the residue LIG is: COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.1HETATM1 C LIG 1 1.481 -1.276 -0.621 1.00 0.00 CHETATM2 C LIG 1 2.216 -2.370 -1.040 1.00 0.00 CHETATM3 S LIG 1 3.770 -2.409 -0.306 1.00 0.00 SHETATM4 C LIG 1 3.456 -0.998 0.609 1.00 0.00 CHETATM5 C LIG 1 2.207 -0.479 0.313 1.00 0.00 CHETATM6 C LIG 1 5.156 0.676 1.386 1.00 0.00 CHETATM7 C LIG 1 4.423 -0.491 1.600 1.00 0.00 CHETATM8 C LIG 1 4.550 -1.119 2.847 1.00 0.00 CHETATM9 C LIG 1 5.256 -0.503 3.905 1.00 0.00 CHETATM 10 C LIG 1 6.107 0.592 3.667 1.00 0.00 CHETATM 11 C LIG 1 6.008 1.181 2.393 1.00 0.00 CHETATM 12 S LIG 1 7.457 2.548 5.198 1.00 0.00 SHETATM 13 C LIG 1 7.220 0.945 4.621 1.00 0.00... I am really thankful Elie -- 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] segmentation fault with mdrun
Dear All I am trying to perform the azide ion in water simulation with Gromacs. I generated to topology file with PRODG server for azide ion and ran the calculations.I got one error at grompp level which was 327 non-matching atom names atom names from azide.top will be used atom names from azide.gro will be ignored I continued with the maxwarn and performed energy minimization which went smoothly.However no sooner I started equilibration in NVT run using mdrun it crashed with segmentation fault. Please help me to locate the error. I went through the previous mails on the mailing list but I could not sort it out. The topology file is : ; Include forcefield parameters #include ffG43a1.itp ;Include azide topology #include azide.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name azide in water [ molecules ] ; Compound#mols SOL 108 AZI 1 and the itp file for azide which I made from PRODG is [ moleculetype ] ; Name nrexcl AZI 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 N 1 AZI N1 1 -1.000 14.0067 2 N 1 AZI N2 12.000 14.0067 3 N 1 AZI N3 1 -1.000 14.0067 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.112 4527362.40.112 4527362.4 ;N2 N1 2 3 20.112 4527362.40.112 4527362.4 ;N2 N3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2180.0 41840001.2180.0 41840001.2 ;N1 N2 N3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] segmentation fault with mdrun
On 8/21/12 6:00 AM, Deepak Ojha wrote: Dear All I am trying to perform the azide ion in water simulation with Gromacs. I generated to topology file with PRODG server for azide ion and ran the calculations.I got one error at grompp level which was 327 non-matching atom names atom names from azide.top will be used atom names from azide.gro will be ignored I continued with the maxwarn and performed energy minimization which went smoothly.However no sooner I started equilibration in NVT run using mdrun it crashed with segmentation fault. Please help me to locate the error. I went through the previous mails on the mailing list but I could not sort it out. Don't use -maxwarn unless you know exactly why you're doing it. The fact that you have 327 non-matching names and 327 atoms in the system (108*3 + 3) suggests the contents of your coordinate file do not match that of the topology in terms of the order of the [molecules] section. Likely your azide should be listed first, presumably if you took the coordinate file for this molecule and solvated it. Also beware that PRODRG topologies are notoriously unreliable and that linear molecules should not be constructed in this way (180 degree angles are not stable). See, for instance, the following tutorial for a more robust method: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html -Justin The topology file is : ; Include forcefield parameters #include ffG43a1.itp ;Include azide topology #include azide.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name azide in water [ molecules ] ; Compound#mols SOL 108 AZI 1 and the itp file for azide which I made from PRODG is [ moleculetype ] ; Name nrexcl AZI 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 N 1 AZI N1 1 -1.000 14.0067 2 N 1 AZI N2 12.000 14.0067 3 N 1 AZI N3 1 -1.000 14.0067 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.112 4527362.40.112 4527362.4 ;N2 N1 2 3 20.112 4527362.40.112 4527362.4 ;N2 N3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2180.0 41840001.2180.0 41840001.2 ;N1 N2 N3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] segmentation fault-g_spatial
Dear D.M. I wrote g_spatial and Justin is correct that you simply need to use a larger number for -nab. It's not a bug per se, it is simply that I didn't write the program to do two loops through the input trajectory (one to determine the required bins and then allocate memory and then another loop to count the values). So it is just quick and dirty coding, but when -nab is sufficiently large it will not be wrong. Here is what happens: let's say that you have a cubic box. You then use trjconv to do a fitting in which you rotate the box differently in different frames. Now the length of the new x-axis in a frame could be the length of the diagonal of your box, which is substantially longer. This is why you need to ask the program to allocate memory for additional bins (which will be written out to your cube file, making it larger, so you don't want to set -nab too much larger than is necessary). Pressure coupling also influences this, but not as much. Note that if you make your bins half as large (for higher resolution) then you will need to double the value that you provide to -nab. I usually use -nab 50. You may need a larger value if you use smaller bins or a very rectangular system which you rotate before running through g_spatial. You may also have to use very large values of -nab if you do a fitting on a system where your central group is not centered (use the suggested trjconv preparation listed in g_spatial -h). Finally, if you are using incredibly small bin sizes, then you might really be running into an out-of-memory condition, although that should not result in a segfault as the program should exit cleanly if it can not allocate the required memory. Chris. Forwarded Message - From: delara aghaie d_aghaie at yahoo.com To: Discussion list for GROMACS users gmx-users at gromacs.org Sent: Tuesday, 19 June 2012, 12:04 Subject: [gmx-users] segmentation fault-g_spatial Dear Gromacs users. I have a protein in a box of water. I want to calculate the SDF of water molecules around the protein. I have used the procedure described in this page: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial after two times using trjconv for putting the protein in the center of box and removing its rotation and translation, I use the g_spatial order. g_spatial -s ~.tpr -f ~.xtc (this is the output .xtc after tao times running trjcov). I get this message: Reading frame 7 time 14.000 There was an item outside of the allocated memory. Increase the value given with the -nab option. Memory was allocated for [-0.374000,-0.301000,-0.217000]to [7.676000,7.749000,7.833000] Memory was required for [-0.375000,6.70,6.815001] 1) I want to know what exactly does (nab) option? 2) I have changed this -nab value from 4 to 6,8,10,.40 but again I get something like the mentioned message or the segmentation fault. What should I do to fix it and is it a limiting value for nab option? 3) Also please let me know, is it possible to calculate SDF of water molecules around a specific residue by creating and index group which contains that residue? Thanks Regards D.M -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Fw: [gmx-users] segmentation fault-g_spatial
- Forwarded Message - From: delara aghaie d_agh...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 19 June 2012, 12:04 Subject: [gmx-users] segmentation fault-g_spatial Dear Gromacs users. I have a protein in a box of water. I want to calculate the SDF of water molecules around the protein. I have used the procedure described in this page: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial after two times using trjconv for putting the protein in the center of box and removing its rotation and translation, I use the g_spatial order. g_spatial -s ~.tpr -f ~.xtc (this is the output .xtc after tao times running trjcov). I get this message: Reading frame 7 time 14.000 There was an item outside of the allocated memory. Increase the value given with the -nab option. Memory was allocated for [-0.374000,-0.301000,-0.217000] to [7.676000,7.749000,7.833000] Memory was required for [-0.375000,6.70,6.815001] 1) I want to know what exactly does (nab) option? 2) I have changed this -nab value from 4 to 6,8,10,.40 but again I get something like the mentioned message or the segmentation fault. What should I do to fix it and is it a limiting value for nab option? 3) Also please let me know, is it possible to calculate SDF of water molecules around a specific residue by creating and index group which contains that residue? Thanks Regards D.M -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] segmentation fault-g_spatial
On 6/19/12 9:34 AM, delara aghaie wrote: - Forwarded Message - *From:* delara aghaie d_agh...@yahoo.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, 19 June 2012, 12:04 *Subject:* [gmx-users] segmentation fault-g_spatial Dear Gromacs users. I have a protein in a box of water. I want to calculate the SDF of water molecules around the protein. I have used the procedure described in this page: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial after two times using trjconv for putting the protein in the center of box and removing its rotation and translation, I use the g_spatial order. g_spatial -s ~.tpr -f ~.xtc (this is the output .xtc after tao times running trjcov). I get this message: Reading frame 7 time 14.000 There was an item outside of the allocated memory. Increase the value given with the -nab option. Memory was allocated for [-0.374000,-0.301000,-0.217000]to [7.676000,7.749000,7.833000] Memory was required for [-0.375000,6.70,6.815001] 1) I want to know what exactly does (nab) option? According to g_spatial -h: BUGS: When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected and the program is halted prior to the fault while displaying a warning message suggesting the use of the -nab (Number of Additional Bins) option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again with an increased -nab value. 2) I have changed this -nab value from 4 to 6,8,10,.40 but again I get something like the mentioned message or the segmentation fault. What should I do to fix it and is it a limiting value for nab option? Maybe try an even larger value. But since it is a known bug, it may simply be that the program needs to be fixed or re-written to work more effectively. 3) Also please let me know, is it possible to calculate SDF of water molecules around a specific residue by creating and index group which contains that residue? Yes, it should be. Try it and see. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault - pdb2gmx specbond.dat
Dear Gmx Users, I created a plane surface made of 4 different atoms (400 atoms togehter). Each atom correspond to different residue - I added them to the aminoacids.rtp file. They are placed in different positions with LJ radius of 1.7A and they their center is 3.6 A away from each other (0.2A between atom LJsurfaces). I want to create bonds between all of them so I added specbonds.dat to my working directory: 10 POSSOD4POSSOD40.36POSPOS POSSOD4NEGCLA40.36POSNEG POSSOD4POLN40.36POSPOL POSSOD4NONC40.36POSNON NEGCLA4NEGCLA40.36NEGNEG NEGCLA4POLN40.36NEGPOL NEGCLA4NONC40.36NEGNON POLN4POLN40.36POLPOL POLN4NONC40.36POLNON NONC4NONC40.36NONNON So that all of them can create bonds with each of them being within the distance of 3.6A. When I process to pdb2gmx where the matrix is created and bonds are being linked when the last residues are linked: . Linking POL-397 N-397 and NEG-398 CLA-398... Linking NEG-398 CLA-398 and NON-399 C-399... Linking NON-399 C-399 and POL-400 N-400... Segmentation fault (core dumped) The Gromacs is installed on the cluster - version 4.5.5. I tried also on 4.5.4. and the same happens. Could you please advise? Steven -- 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] segmentation fault during equilibration
Dear gmx users, I am simulating a system including carbon nanotube(a finite one)+water+surfactant and so far I have done these things: 1.I generated the topology of CNT ( opls force field) by this command: g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT 2.I used TopolGen to produce topology of surfactant and I calculated the charges of atomes by the RESP method and checked the atomtypes to make sure that they make sence as well.so I changed some atomtypes according to the opls. 3.I build a topol.top file that contains topolgy of CNT+surfactant. 4.I created the initial configuration for the CNT+surfactant by means of packmol. 5.I used editconf and genbox with these command: editconf -f CNTSUR.pdb -o newbox.gro -d 0.7 -bt cubic genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro 6.I run grompp and genion for adding the ions: grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -p topol.top -o solv_ions.gro -nname BR -nn 28 7.I run grompp again for energy minimization: grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr mdrun -deffnm em the em_real.mdp file contains: ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 7 ; Maximum number of (minimization) steps to perform energygrps = UNK LIG ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 0.9 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 0.9 ; long range electrostatic cut-off rvdw= 1.4 ; Periodic Boundary Conditions (yes/no) pbc = xyz ; Periodic Boundary Conditions (yes/no) 8.then I made an index file for CNT and surfactant and used genrestr to restraint the CNT and surfactant during equilibration. 9.I run grompp and mdrun with these command:grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -n index.ndx mdrun -deffnm nvt and after passing 42900 of 5 steps, segmentation fault occured.I checked the log file but it did not contain any errors and I also used VMD to see trajetory but I did not see anything wrong. I would be pleased if anyone could help me how to fix this. -- 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] segmentation fault during equilibration
On 5/1/12 7:19 AM, niaz poorgholami wrote: Dear gmx users, I am simulating a system including carbon nanotube(a finite one)+water+surfactant and so far I have done these things: 1.I generated the topology of CNT ( opls force field) by this command: g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT 2.I used TopolGen to produce topology of surfactant and I calculated the charges of atomes by the RESP method and checked the atomtypes to make sure that they make sence as well.so I changed some atomtypes according to the opls. 3.I build a topol.top file that contains topolgy of CNT+surfactant. 4.I created the initial configuration for the CNT+surfactant by means of packmol. 5.I used editconf and genbox with these command: editconf -f CNTSUR.pdb -o newbox.gro -d 0.7 -bt cubic Unrelated to the crash, but if your longest cutoff is 1.4 nm, setting a solute-box distance of 0.7 nm will lead to trouble if you ever use NPT. With just a small fluctuation in box dimension, you can easily violate the minimum image convention. genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro 6.I run grompp and genion for adding the ions: grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -p topol.top -o solv_ions.gro -nname BR -nn 28 7.I run grompp again for energy minimization: grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr mdrun -deffnm em the em_real.mdp file contains: ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 7 ; Maximum number of (minimization) steps to perform energygrps = UNK LIG ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 0.9 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 0.9 ; long range electrostatic cut-off rvdw= 1.4 ; Periodic Boundary Conditions (yes/no) pbc = xyz ; Periodic Boundary Conditions (yes/no) What was the outcome of EM? What were your values for Fmax and Epot? 8.then I made an index file for CNT and surfactant and used genrestr to restraint the CNT and surfactant during equilibration. 9.I run grompp and mdrun with these command:grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -n index.ndx mdrun -deffnm nvt and after passing 42900 of 5 steps, segmentation fault occured.I checked the log file but it did not contain any errors and I also used VMD to see trajetory but I did not see anything wrong. I would be pleased if anyone could help me how to fix this. We need to see your complete .mdp file for the NVT run. As of now, there is no indication of what is wrong. -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] segmentation fault during equilibration
thank you Sir for your reply.below I provide you .mdp file: title = UNK-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG ; Run parameters integrator = md; leap-frog integrator nsteps = 5; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = UNK LIG ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = UNK_LIG Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed -- 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] segmentation fault during equilibration
On 5/1/12 1:13 PM, niaz poorgholami wrote: thank you Sir for your reply.below I provide you .mdp file: title = UNK-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG ; Run parameters integrator = md; leap-frog integrator nsteps = 5; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps Your .trr files will be huge with these settings. I would only recommend getting such output every step if your system were collapsing within just a few steps, but not in this case. Though, if you have such output, watching the trajectory (provided your workstation doesn't run out of memory) should point to the problem. nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = UNK LIG ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = UNK_LIG Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed I see nothing particularly glaring with the .mdp file that would be causing a problem. You also did not answer my question about EM, so it is still a possibility that the system is insufficiently minimized, but that's just a guess since I don't know. Otherwise: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -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] segmentation fault during equilibration
Dear Justin the results of EM was: Steepest Descents converged to Fmax 1000 in 77 steps Potential Energy = -3.6802272e+05 Maximum force = 8.9652832e+02 on atom 1556 Norm of force = 1.1512711e+02 thank you for your concern -- 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] segmentation fault during equilibration
On 5/1/12 2:50 PM, niaz poorgholami wrote: Dear Justin the results of EM was: Steepest Descents converged to Fmax 1000 in 77 steps Potential Energy = -3.6802272e+05 Maximum force = 8.9652832e+02 on atom 1556 Norm of force = 1.1512711e+02 thank you for your concern All of that seems fine. You'll have to investigate using the tips I linked before. It is also possible that your topology is unstable. The procedure you described before seems reasonable, but thorough parameterization can be very tricky and may require refinement. -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] segmentation fault
priya thiyagarajan wrote: hello sir, thanks for your kind reply.. in another folder i resubmitted my mdrun from starting time.. i reduced my time step.. i kept my time step = 0.001 this is my md.mdp file title= Gromacs43a1 lipopeptide MD ; Run parameters integrator= md; leap-frog integrator nsteps= 500; 1 * 500 = 5000 ps, 5 ns dt= 0.001; 1 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.4; short-range neighborlist cutoff (in nm) rcoulomb= 1.4; short-range electrostatic cutoff (in nm) rvdw= 1.4; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= *V-rescale*; modified Berendsen thermostat tc-grps= DRG SOL; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off i resubmitted my mdrun and my run completed i analysed my output file.. now it completed at 1.286ns out of 5ns.. in log file it didnt give any information about this error.. in error file its showing segmentation fault.. how to solve this prolem.. Mark already provided this link, but I'll post it again anyway: http://www.gromacs.org/Documentation/Terminology/Blowing_Up On that page you will find not only several possibilities as to the source of the problem, but also the means to diagnose what might be going wrong. Please pay careful attention to this page, as it summarizes this information very well. is it only because of some problem in my system?? Yes, quite likely. The questions that come to mind for me - what is DRG? What is its topology? Did you do proper energy minimization and equilibration? -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] Segmentation Fault using g_cluster
On 28/03/2012 2:14 PM, Davide Mercadante wrote: Thank you for the prompt reply.! Indeed, I am using Gromacs version 4.5.5 compiled in double-precision and I am running the analysis on a MacBook PRO. I tried to open an issue at http://redmine/gromacs.org but it asks me for login name and passwd which I don't think I have as I never subscribed as developer. I may be wrong though..do I need to register? Yes, just sign up. We need to be able to contact you to let you know the solution or get more information, so anonymous bug submission is not very useful. I suppose that if this is not an explainable issue at the moment there is no solution to it? The problem with plain segfaulting is that there's no way to tell what caused the problem. GROMACS tries hard not to do this, but clearly it's not perfect. There may be a code bug. There may be a way for you to use the code better. We just don't know yet. There's certainly room to improve the code. Mark Thank you again for the reply. It has been much appreciated. Davide From: Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Date: Wed, 28 Mar 2012 13:29:40 +1100 To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] Segmentation Fault using g_cluster On 28/03/2012 1:00 PM, Davide Mercadante wrote: Dear Gromacs Users, I am trying to run g_cluster to find an average structure for my system and after giving the following command line: g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n --g g_cluster started without problems and continued calculating the matrix etc...until I got this: Last frame 5000 time 5.004 Allocated 645448320 bytes for frames Read 5001 frames from trajectory allnj10_XM10.xtc Computing 5001x5001 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from 0.0816802 to 0.301369 nm Average RMSD is 0.208468 Number of structures for matrix 5001 Energy of the matrix is 364.532 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802 Linking structures ** Sorting and renumbering clusters Found 1425 clusters Writing middle structure for each cluster to pdb_ligplot_XM.pdb Segmentation fault: 11 Can you please help me to understand where the problem comes from and how I can solve it? Any help is greatly appreciated. I don't think this should happen. You haven't stated your GROMACS version. If you can reproduce this with 4.5.5., please open an issue here http://redmine.gromacs.org/ and upload your files and instructions on how to reproduce the problem. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Segmentation Fault using g_cluster
Dear Gromacs Users, I am trying to run g_cluster to find an average structure for my system and after giving the following command line: g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n g g_cluster started without problems and continued calculating the matrix etcuntil I got this: Last frame 5000 time 5.004 Allocated 645448320 bytes for frames Read 5001 frames from trajectory allnj10_XM10.xtc Computing 5001x5001 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from 0.0816802 to 0.301369 nm Average RMSD is 0.208468 Number of structures for matrix 5001 Energy of the matrix is 364.532 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802 Linking structures ** Sorting and renumbering clusters Found 1425 clusters Writing middle structure for each cluster to pdb_ligplot_XM.pdb Segmentation fault: 11 Can you please help me to understand where the problem comes from and how I can solve it? Any help is greatly appreciated. Thank you. Davide -- 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] Segmentation Fault using g_cluster
On 28/03/2012 1:00 PM, Davide Mercadante wrote: Dear Gromacs Users, I am trying to run g_cluster to find an average structure for my system and after giving the following command line: g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n --g g_cluster started without problems and continued calculating the matrix etc...until I got this: Last frame 5000 time 5.004 Allocated 645448320 bytes for frames Read 5001 frames from trajectory allnj10_XM10.xtc Computing 5001x5001 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from 0.0816802 to 0.301369 nm Average RMSD is 0.208468 Number of structures for matrix 5001 Energy of the matrix is 364.532 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802 Linking structures ** Sorting and renumbering clusters Found 1425 clusters Writing middle structure for each cluster to pdb_ligplot_XM.pdb Segmentation fault: 11 Can you please help me to understand where the problem comes from and how I can solve it? Any help is greatly appreciated. I don't think this should happen. You haven't stated your GROMACS version. If you can reproduce this with 4.5.5., please open an issue here http://redmine.gromacs.org/ and upload your files and instructions on how to reproduce the problem. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation Fault using g_cluster
Thank you for the prompt reply.! Indeed, I am using Gromacs version 4.5.5 compiled in double-precision and I am running the analysis on a MacBook PRO. I tried to open an issue at http://redmine/gromacs.org but it asks me for login name and passwd which I don't think I have as I never subscribed as developer. I may be wrong though..do I need to register? I suppose that if this is not an explainable issue at the moment there is no solution to it? Thank you again for the reply. It has been much appreciated. Davide From: Mark Abraham mark.abra...@anu.edu.au Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wed, 28 Mar 2012 13:29:40 +1100 To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Segmentation Fault using g_cluster On 28/03/2012 1:00 PM, Davide Mercadante wrote: Dear Gromacs Users, I am trying to run g_cluster to find an average structure for my system and after giving the following command line: g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n g g_cluster started without problems and continued calculating the matrix etcuntil I got this: Last frame 5000 time 5.004 Allocated 645448320 bytes for frames Read 5001 frames from trajectory allnj10_XM10.xtc Computing 5001x5001 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from 0.0816802 to 0.301369 nm Average RMSD is 0.208468 Number of structures for matrix 5001 Energy of the matrix is 364.532 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802 Linking structures ** Sorting and renumbering clusters Found 1425 clusters Writing middle structure for each cluster to pdb_ligplot_XM.pdb Segmentation fault: 11 Can you please help me to understand where the problem comes from and how I can solve it? Any help is greatly appreciated. I don't think this should happen. You haven't stated your GROMACS version. If you can reproduce this with 4.5.5., please open an issue here http://redmine.gromacs.org/ and upload your files and instructions on how to reproduce the problem. 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 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] Segmentation fault
Hi all Would you please let me know how can I remove the following error when I want to run 'mdrun -v -deffnm H'? Back Off! I just backed up H.log to ./#H.log.1# Getting Loaded... Reading file H.tpr, VERSION 4.5.4 (single precision) Starting 24 threads Segmentation fault Thanks Regards Saly -- 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] Segmentation fault
saly jackson wrote: Hi all Would you please let me know how can I remove the following error when I want to run 'mdrun -v -deffnm H'? Back Off! I just backed up H.log to ./#H.log.1# Getting Loaded... Reading file H.tpr, VERSION 4.5.4 (single precision) Starting 24 threads Segmentation fault Your simulation crashed. The fact that it did so immediately suggests inadequate energy minimization and/or equilibration. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -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] Segmentation fault
Hi , Thank you for help. I solve my problem for LINCS error But now I have another problem after mdrun command gromacs output Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Martini system from nap.pdb' 5000 steps,100.0 ps. step 0Segmentation fault Please give the valuable suggestion.. 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] Segmentation fault
On 9/03/2012 6:24 PM, rama david wrote: Hi , Thank you for help. I solve my problem for LINCS error But now I have another problem after mdrun command gromacs output Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Martini system from nap.pdb' 5000 steps,100.0 ps. step 0Segmentation fault No idea. Look at your stdout and/or log files and then consult the errors page of the GROMACS webpage. 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] segmentation fault err
Dear gmx-users, I'm facing segmentation fault error while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values, potential energy etc. are not changing much so i guess this is the cause for fatal error. But I can't figure out the reason behind sudden increase in temperature. I'm using following options in my mdp file: ;Temperature coupling tc-grps = system tau_t = 1.0 ; Temperature coupling time constant. ref_t = 50.0 ; In reduced units ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 50.0 Can anybody suggest me, if i'm missing something (to take care of)? Regards, Shilpa -- 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] segmentation fault err
On 6/03/2012 2:58 AM, shilpa yadahalli wrote: Dear gmx-users, I'm facing segmentation fault error while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values, potential energy etc. are not changing much so i guess this is the cause for fatal error. But I can't figure out the reason behind sudden increase in temperature. I'm using following options in my mdp file: ;Temperature coupling tc-grps = system tau_t = 1.0 ; Temperature coupling time constant. ref_t = 50.0 ; In reduced units ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 50.0 Can anybody suggest me, if i'm missing something (to take care of)? You will need to look at the end of the .log and/or stdout file to know, but probably this is what is happening http://www.gromacs.org/Documentation/Terminology/Blowing_Up 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] Segmentation fault - Implicit solvent
Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? thank you Steven -- 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] Segmentation fault - Implicit solvent
Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -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] Segmentation fault - Implicit solvent
On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/**issues/777http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem? Steven -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Segmentation fault - Implicit solvent
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.comwrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/**issues/777http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem? Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g. 12 nodes? Steven Steven -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Segmentation fault - Implicit solvent
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.comwrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.comwrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.eduwrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/**issues/777http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem? Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g. 12 nodes? Sorry, the same problem : Initial temperature: 298.398 K Started mdrun on node 0 Thu Mar 1 15:56:04 2012 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.27391e+02 4.27461e+02 1.27733e+03 2.73432e+01 -6.95645e+02 GB Polarization Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR) inf 3.59121e+02 6.85627e+02 3.68572e+04 -7.57140e+02 Coulomb (SR) Potential Kinetic En. Total Energy Conserved En. -3.30643e+04 inf nan nan nan Temperature Pressure (bar) nan 0.0e+00 - ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Segmentation fault - Implicit solvent
Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem? Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g. 12 nodes? Sorry, the same problem : I think, as stated in the redmine issue cited before, the limit is 2 threads/processors. -Justin Initial temperature: 298.398 K Started mdrun on node 0 Thu Mar 1 15:56:04 2012 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.27391e+02 4.27461e+02 1.27733e+03 2.73432e+01 -6.95645e+02 GB Polarization Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR) inf 3.59121e+02 6.85627e+02 3.68572e+04 -7.57140e+02 Coulomb (SR) Potential Kinetic En. Total Energy Conserved En. -3.30643e+04 inf nan nan nan Temperature Pressure (bar) nan 0.0e+00 - ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing
Re: [gmx-users] Segmentation fault - Implicit solvent
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.commailto: s.neuman...@gmail.com** wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com** wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/__**issues/777http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/**issues/777http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem? Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g. 12 nodes? Sorry, the same problem : I think, as stated in the redmine issue cited before, the limit is 2 threads/processors. -Justin I tried on one thread and on two threads and the error is still the same. Without particle decomposition the problem remains. Any suggestions? Steven Initial temperature: 298.398 K Started mdrun on node 0 Thu Mar 1 15:56:04 2012 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.27391e+02 4.27461e+02 1.27733e+03 2.73432e+01 -6.95645e+02 GB Polarization Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR) inf 3.59121e+02 6.85627e+02 3.68572e+04 -7.57140e+02 Coulomb (SR) Potential Kinetic En. Total Energy Conserved En. -3.30643e+04 inf nan nan nan Temperature Pressure (bar) nan 0.0e+00 - ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia
Re: [gmx-users] Segmentation fault - Implicit solvent
Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__ wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__ wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/issues/777 http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem? Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g. 12 nodes? Sorry, the same problem : I think, as stated
Re: [gmx-users] Segmentation fault - Implicit solvent
On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com**__ wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com**__ wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/___**_issues/777http://redmine.gromacs.org/issues/777 http://redmine.gromacs.org/__**issues/777http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/__**issues/777http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/**issues/777http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will
Re: [gmx-users] Segmentation fault - Implicit solvent
On 2/03/2012 9:22 AM, Steven Neumann wrote: On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__ wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__ wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1#
Re: [gmx-users] Segmentation fault - Implicit solvent
On Thu, Mar 1, 2012 at 10:26 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 2/03/2012 9:22 AM, Steven Neumann wrote: On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__ wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__ wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Bond parameters continuation = no constraints = none ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) ; Infinite box with no cutoffs pbc = no rcoulomb = 0 ; short-range electrostatic cutoff (in nm) coulombtype = cut-off vdwtype = cut-off rvdw = 0 ; short-range van der Waals cutoff (in nm) epsilon_rf = 0 comm_mode = angular ; remove angular and com motions ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80.0 sa_surface_tension = 2.25936 rgbradii = 0 sa_algorithm = Ace-approximation nstgbradii = 1 ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 298 ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 298.0 gen_seed = -1 Then after grompp I am trying to run the simulation on the cluster: mdrun -pd -deffnm nvt500ps My log file: Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# starting mdrun 'Protein' 100 steps, 500.0 ps. Segmentation fault Do you have any clue what is happening? Try running in serial or with a maximum of 2 threads. Your problem could be related to http://redmine.gromacs.org/issues/777 http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/__issues/777 http://redmine.gromacs.org/issues/777. You will need to upgrade to 4.5.5 (serial should work on 4.5.4). -Justin Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem?
[gmx-users] Segmentation fault
Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Segmentation fault (core dumped) saba@linuxserver:~/complex/MD I used the command : ulimit -s unlimited ulimit -c unlimited but no vain, the problem still persists, Tell me how to fix it? I urgently need to study secondary structure during simulations Thanks... -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Segmentation fault
On 2/01/2012 12:35 AM, Saba Ferdous wrote: Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Segmentation fault (core dumped) saba@linuxserver:~/complex/MD I used the command : ulimit -s unlimited ulimit -c unlimited but no vain, the problem still persists, Tell me how to fix it? Assuming other GROMACS tools work, you've done something wrong with the DSSP installation, but it's impossible for us to say what. Note that the version of DSSP released on the last year or two is unsuitable - get the old one. 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] Segmentation fault error from mdrun
Hi, I encounter the following error when trying to execute mdrun: # Running Gromacs: read TPR and write output to /gpfs disk $MPIRUN $MDRUN -v -nice 0 -np $NSLOTS \ -s n12_random_50_protein_all.tpr \ -o n12_random_50_protein_all.trr \ -c n12_random_50_protein_all.gro \ -g n12_random_50_protein_all.log \ -x n12_random_50_protein_all.xtc \ -e n12_random_50_protein_all.edr Error: [compute-0-7:12377] Failing at address: 0x7159fd0 [compute-0-30:07435] [ 1] mdrun [0x761971] [compute-0-30:07435] *** End of error message *** [compute-0-29:15535] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15535] [ 1] mdrun [0x761d60] [compute-0-29:15535] *** End of error message *** [compute-1-29:19799] [ 0] /lib64/libpthread.so.0 [0x33aac0e7c0] [compute-1-29:19799] [ 1] mdrun [0x762065] [compute-1-29:19799] *** End of error message *** [compute-0-29:15537] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15537] [ 1] mdrun [0x762065] [compute-0-29:15537] *** End of error message *** [compute-0-29:15536] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15536] [ 1] mdrun [0x762065] [compute-0-29:15536] *** End of error message *** [compute-1-31:11981] [ 0] /lib64/libpthread.so.0 [0x374f00e7c0] [compute-1-31:11981] [ 1] mdrun [0x761d60] [compute-1-31:11981] *** End of error message *** [compute-1-31:11982] [ 0] /lib64/libpthread.so.0 [0x374f00e7c0] [compute-1-31:11982] [ 1] mdrun [0x761960] [compute-1-31:11982] *** End of error message *** [compute-0-29:15538] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15538] [ 1] mdrun [0x761960] [compute-0-29:15538] *** End of error message *** [compute-0-7:12377] [ 0] /lib64/libpthread.so.0 [0x387c60e7c0] [compute-0-7:12377] [ 1] mdrun [0x729641] [compute-0-7:12377] *** End of error message *** [compute-1-29:19796] [ 0] /lib64/libpthread.so.0 [0x33aac0e7c0] [compute-1-29:19796] [ 1] mdrun [0x762065] [compute-1-29:19796] *** End of error message *** [compute-1-31.local][[50630,1],32][btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) -- mpirun noticed that process rank 35 with PID 32477 on node compute-1-8.local exited on signal 11 (Segmentation fault). -- This is a parallel job that caused segmentation fault on compute-1-8, thus causing the entire job to fail. Any input would be most appreciated. Lily -- 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] Segmentation fault error from mdrun
On 8/12/2011 7:36 AM, rainy908 wrote: Hi, I encounter the following error when trying to execute mdrun: # Running Gromacs: read TPR and write output to /gpfs disk $MPIRUN $MDRUN -v -nice 0 -np $NSLOTS \ -s n12_random_50_protein_all.tpr \ -o n12_random_50_protein_all.trr \ -c n12_random_50_protein_all.gro \ -g n12_random_50_protein_all.log \ -x n12_random_50_protein_all.xtc \ -e n12_random_50_protein_all.edr You can save yourself some typing with mdrun -deffnm. Also note that mdrun -np does nothing for GROMACS 4.x. Error: [compute-0-7:12377] Failing at address: 0x7159fd0 [compute-0-30:07435] [ 1] mdrun [0x761971] [compute-0-30:07435] *** End of error message *** [compute-0-29:15535] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15535] [ 1] mdrun [0x761d60] [compute-0-29:15535] *** End of error message *** [compute-1-29:19799] [ 0] /lib64/libpthread.so.0 [0x33aac0e7c0] [compute-1-29:19799] [ 1] mdrun [0x762065] [compute-1-29:19799] *** End of error message *** [compute-0-29:15537] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15537] [ 1] mdrun [0x762065] [compute-0-29:15537] *** End of error message *** [compute-0-29:15536] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15536] [ 1] mdrun [0x762065] [compute-0-29:15536] *** End of error message *** [compute-1-31:11981] [ 0] /lib64/libpthread.so.0 [0x374f00e7c0] [compute-1-31:11981] [ 1] mdrun [0x761d60] [compute-1-31:11981] *** End of error message *** [compute-1-31:11982] [ 0] /lib64/libpthread.so.0 [0x374f00e7c0] [compute-1-31:11982] [ 1] mdrun [0x761960] [compute-1-31:11982] *** End of error message *** [compute-0-29:15538] [ 0] /lib64/libpthread.so.0 [0x39df60e7c0] [compute-0-29:15538] [ 1] mdrun [0x761960] [compute-0-29:15538] *** End of error message *** [compute-0-7:12377] [ 0] /lib64/libpthread.so.0 [0x387c60e7c0] [compute-0-7:12377] [ 1] mdrun [0x729641] [compute-0-7:12377] *** End of error message *** [compute-1-29:19796] [ 0] /lib64/libpthread.so.0 [0x33aac0e7c0] [compute-1-29:19796] [ 1] mdrun [0x762065] [compute-1-29:19796] *** End of error message *** [compute-1-31.local][[50630,1],32][btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) -- mpirun noticed that process rank 35 with PID 32477 on node compute-1-8.local exited on signal 11 (Segmentation fault). -- This is a parallel job that caused segmentation fault on compute-1-8, thus causing the entire job to fail. You need to look at stderr, stdout (some of which are above) and the .log file to find out what GROMACS thought caused the crash. You also need to use an mpi-enabled mdrun. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault from power6 kernel
Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Fabio The most likely issue is some normal blowing up scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. Mark -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] segmentation fault from power6 kernel
On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Please file a report here http://redmine.gromacs.org http://redmine.gromacs.org/ including your observations and a .tpr that will reproduce them. Thanks, Mark Fabio The most likely issue is some normal blowing up scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault from power6 kernel
Hi Mark, today I tested the 4.5.5 version. It seems here there's not that problem. Anyway, I will take some days to make more tests. Thank you, Fabio - Messaggio originale - Da: Mark Abraham mark.abra...@anu.edu.au A: Discussion list for GROMACS users gmx-users@gromacs.org Inviato: Giovedì, 3 novembre 2011 14:40:39 Oggetto: Re: [gmx-users] segmentation fault from power6 kernel On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Please file a report here http://redmine.gromacs.org including your observations and a .tpr that will reproduce them. Thanks, Mark Fabio The most likely issue is some normal blowing up scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. 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 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] segmentation fault from power6 kernel
Dear all,
I've trying to run a simulation on a IBM Power6 cluster. At the
beginning of the simulation I've got a segmentation fault. I investigated with
TotalView and I've found that this segmentation violation originates in the
pwr6kernel310.F
Up to now, I still didn't find what is behind this seg violation. I would like
to ask if anybody is aware of a bug behind this function.
The simulation is obtained by using Gromacs 4.5.3 compiled in double precision.
The options that I specified in the configure are:
--disable-threads --enable-power6 --enable-mpi
The log file doesn't provide much informations:
Log file opened on Wed Nov 2 20:11:02 2011
Host: sp0202 pid: 11796682 nodeid: 0 nnodes: 1
The Gromacs distribution was built Thu Dec 16 14:44:40 GMT+01:00 2010 by
propro01@sp0201 (AIX 1 00C3E6444C00)
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.5.3 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = md
nsteps = 250
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 2500
nstxout = 2500
nstvout = 2500
nstfout = 0
nstcalcenergy= 10
nstenergy= 2500
nstxtcout= 2500
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 50
nky = 50
nkz = 50
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Nose-Hoover
nsttcouple = 10
epc = No
epctype = Isotropic
nstpcouple = -1
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist
[gmx-users] Segmentation fault
Hi When i perform mdrun for energy minimization, I found an error revealed segmentation fault. Please explain me -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault after mdrun for MD simulation
Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.048739, max 1.100685 (between atoms 8422 and 8421) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length .. .. snip .. .. starting mdrun 'TUBULIN ALPHA CHAIN' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 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 .. .. snip .. .. step 0: Water molecule starting at atom 23781 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1# Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2# Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2# Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21: 1473 Segmentation fault (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr On 16 August 2011 10:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Hi, I get the error Atomtype CR1 not found when I execute grompp. After perusing the gmx archives, I understand this error has to do with the lack of CR1 being specified in the force field. However, I did include the appropriate .itp files in my .top file (shown below). As you can see, obviously CR1 is specified in taxol.itp and gtp.itp. Therefore, I'm not sure what exactly is the problem here. You're mixing and matching force fields.
Re: [gmx-users] Segmentation fault after mdrun for MD simulation
rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length If mdrun is failing at step 0, it indicates that your system is physically unreasonable. Either the starting configuration has atomic clashes that have not been resolved (and thus you need better EM and/or equilibration) or that the parameters assigned to the molecules in your system are unreasonable. -Justin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.048739, max 1.100685 (between atoms 8422 and 8421) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length .. .. snip .. .. starting mdrun 'TUBULIN ALPHA CHAIN' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 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 .. .. snip .. .. step 0: Water molecule starting at atom 23781 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1# Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2# Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2# Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21: 1473 Segmentation fault (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr On 16 August 2011 10:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Hi, I get the error Atomtype CR1 not found when I execute grompp. After perusing the gmx archives, I
Re: [gmx-users] Segmentation fault after mdrun for MD simulation
Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em.tpr, VERSION 4.5.3 (single precision) Starting 24 threads Will use 15 particle-particle and 9 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 2.92429 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I figure the problem must lie within my em.mdp file: title = 1JFF cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 ~ I figure this is an issue related to with PME and the Fourier spacing? Thanks, rainy908 On 17 August 2011 17:55, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length If mdrun is failing at step 0, it indicates that your system is physically unreasonable. Either the starting
Re: [gmx-users] Segmentation fault after mdrun for MD simulation
On 18/08/2011 2:41 PM, rainy908 wrote: Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em.tpr, VERSION 4.5.3 (single precision) Starting 24 threads Will use 15 particle-particle and 9 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 2.92429 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I figure the problem must lie within my em.mdp file: It could, but if you follow the above advice you will learn about some other considerations. Mark title = 1JFF cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 ~ I figure this is an issue related to with PME and the Fourier spacing? Thanks, rainy908 On 17 August 2011 17:55, Justin A. Lemkuljalem...@vt.edu wrote: rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30
[gmx-users] Segmentation fault
Hello All, I was trying to run a MD simulation of a 17 amino acid peptide. At the position restraint step, the program crashed after running ~536 ps. It gave the error message: t=536.242 ps: Water molecule starting at atom 6101 cannot be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates. So I looked into the pdb files for atom 6101: In the last but one step, the pdb file looks like: ATOM 6101 OW SOL 1970 44.896 30.613 17.849 1.00 0.00 ATOM 6102 HW1 SOL 1970 45.375 30.296 18.668 1.00 0.00 ATOM 6103 HW2 SOL 1970 44.264 29.904 17.537 1.00 0.00 In the last step, the pdb file looks like: ATOM 6101 OW SOL 1970 395154652137521152.000-290190255628222464.000695407981780533248.000 1.00 0.00 ATOM 6102 HW1 SOL 1970 -2104656020830683136.0005806908484133847040.000-6427192471385538560.000 1.00 0.00 ATOM 6103 HW2 SOL 1970 1131095442881249280.000593978790032441344.0001018902650772520960.000 1.00 0.00 So, there is clearly something wrong. What should I do now to solve this problem? Thanks, Sayan. -- Sayan Bagchi -- 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] Segmentation fault
Sayan Bagchi wrote: Hello All, I was trying to run a MD simulation of a 17 amino acid peptide. At the position restraint step, the program crashed after running ~536 ps. It gave the error message: t=536.242 ps: Water molecule starting at atom 6101 cannot be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates. So I looked into the pdb files for atom 6101: In the last but one step, the pdb file looks like: ATOM 6101 OW SOL 1970 44.896 30.613 17.849 1.00 0.00 ATOM 6102 HW1 SOL 1970 45.375 30.296 18.668 1.00 0.00 ATOM 6103 HW2 SOL 1970 44.264 29.904 17.537 1.00 0.00 In the last step, the pdb file looks like: ATOM 6101 OW SOL 1970 395154652137521152.000-290190255628222464.000695407981780533248.000 1.00 0.00 ATOM 6102 HW1 SOL 1970 -2104656020830683136.0005806908484133847040.000-6427192471385538560.000 1.00 0.00 ATOM 6103 HW2 SOL 1970 1131095442881249280.000593978790032441344.0001018902650772520960.000 1.00 0.00 So, there is clearly something wrong. What should I do now to solve this problem? http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -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] segmentation fault.
dear gmx-users, During equilibriation i get the following error.Any suggestions please. *grompp* WARNING 1 [file npt.mdp]: The sum of the two largest charge group radii (2.369582) is larger than rlist (1.00) This run will generate roughly 73 Mb of data There was 1 warning Back Off! I just backed up npt.tpr to ./#npt.tpr.5# gcq#113: I Don't Like Dirt (The Breeders) * mdrun* WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential Making 1D domain decomposition 2 x 1 x 1 Back Off! I just backed up npt.trr to ./#npt.trr.6# Back Off! I just backed up ener.edr to ./#ener.edr.23# starting mdrun 'NA SODIUM ION in water' 5 steps, 50.0 ps. step 0: Water molecule starting at atom 6153 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.23# step 0: Water molecule starting at atom 4410 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.23# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.23# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.23# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates *Segmentation fault* *mdp file* title = nacl define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.001 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = user energygrps = Na Cl Sol energygrp_table = Na Cl vdwtype= user fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = SOL Na Cl ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel= yes gen_temp= 300.0 gen_seed= -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] segmentation fault.
sreelakshmi ramesh wrote: dear gmx-users, During equilibriation i get the following error.Any suggestions please. *grompp* WARNING 1 [file npt.mdp]: The sum of the two largest charge group radii (2.369582) is larger than rlist (1.00) This message suggests your topology is somehow broken. This run will generate roughly 73 Mb of data There was 1 warning Back Off! I just backed up npt.tpr to ./#npt.tpr.5# gcq#113: I Don't Like Dirt (The Breeders) * mdrun* WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential This still indicates a problem with the table. Take Chris' advice and try your simulation without tabulated potentials. This will tell you whether the problem is from a bad starting structure or because your tables are somehow not usable. Making 1D domain decomposition 2 x 1 x 1 Back Off! I just backed up npt.trr to ./#npt.trr.6# Back Off! I just backed up ener.edr to ./#ener.edr.23# starting mdrun 'NA SODIUM ION in water' 5 steps, 50.0 ps. step 0: Water molecule starting at atom 6153 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.23# step 0: Water molecule starting at atom 4410 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.23# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.23# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.23# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates *Segmentation fault* Step 0 failures indicate either (1) your starting configuration is unreasonable, (2) your .mdp settings are inappropriate, or (3) the tabulated potential is causing the system to collapse. Did you do energy minimization? Was it successful? Good EM is the way around point 1. *mdp file* title = nacl define = -DPOSRES ; position restrain the protein What are you restraining? snip tc-grps = SOL Na Cl ; two coupling groups - more accurate Never couple solvent and ions separately. This alone can be a reason for instability. http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do -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] segmentation fault: g_velacc
Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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] segmentation fault: g_velacc
Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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] segmentation fault: g_velacc
Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] segmentation fault: g_velacc
Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] segmentation fault: g_velacc
Thanks very much, Dr. Kutzner! On Tue, Feb 1, 2011 at 9:14 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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] segmentation fault while running eneconv
Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt Since my simulation was interrupted several times, every time I relaunched it simply doing: mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4 At the end of these simulations I obtained the following files: - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until 50ns - md2_50ns_2.xtc and .edr: files obtained by restarting the previous dynamics that was interrupted before 50 ns - md2_50ns_3.xtc and .edr: same as before - md2_50ns_4.xtc and .edr: same as before After all these runs, I want to concatenate all the dynamics in order to have a single .xtc file md_50ns_tot and a single .edr file md_50ns_tot.edr. For the first, I used: trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc md2_50ns_4.xtc -o md_50ns_tot.xtc and all worked fine: I obtained the output file with no errors (there are no errors also in the .log files) On the contrary, when I tried to do the same with eneconv: eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr md2_50ns_4.edr -o md_50ns_tot.edr I obtained the following output: Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Reading energy frame 1 time 100.000 Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file Reading energy frame 0 time0.000 Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file Reading energy frame 0 time 14900.000 Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file Reading energy frame 0 time 27800.000 Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file Reading energy frame 0 time 38800.000 Summary of files and start times used: FileStart time - 2GH9openmod4_pH10_5ns.edr0.000 2GH9openmod4_pH10_50ns.edr0.000 2GH9openmod4_pH10_50ns_2.part0002.edr14900.000 2GH9openmod4_pH10_50ns_3.part0003.edr27800.000 2GH9openmod4_pH10_50ns_4.part0004.edr38800.000 Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Segmentation fault Looking for some hints in the gmx-users list the only thing I found that could be similar to my problem is this old message: http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html I see in the output error message that the start time for the first two simulations is the same: could be this one the problem for my system? However, I did use tpbconv each time to make restarts of my simulations, I really don't know why the start time is 0.000 in the first two cases. Is there a problem in the results of simulations if these two simulations have the same start time? Practically, what can I do to concatenate my .edr files? Many thanks in advance and best regards Anna Marabotti Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man -- 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] segmentation fault while running eneconv
Anna Marabotti wrote: Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt Since my simulation was interrupted several times, every time I relaunched it simply doing: mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4 At the end of these simulations I obtained the following files: - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until 50ns - md2_50ns_2.xtc and .edr: files obtained by restarting the previous dynamics that was interrupted before 50 ns - md2_50ns_3.xtc and .edr: same as before - md2_50ns_4.xtc and .edr: same as before After all these runs, I want to concatenate all the dynamics in order to have a single .xtc file md_50ns_tot and a single .edr file md_50ns_tot.edr. For the first, I used: trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc md2_50ns_4.xtc -o md_50ns_tot.xtc and all worked fine: I obtained the output file with no errors (there are no errors also in the .log files) On the contrary, when I tried to do the same with eneconv: eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr md2_50ns_4.edr -o md_50ns_tot.edr I obtained the following output: Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Reading energy frame 1 time 100.000 Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file Reading energy frame 0 time0.000 Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file Reading energy frame 0 time 14900.000 Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file Reading energy frame 0 time 27800.000 Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file Reading energy frame 0 time 38800.000 Summary of files and start times used: FileStart time - 2GH9openmod4_pH10_5ns.edr0.000 2GH9openmod4_pH10_50ns.edr0.000 2GH9openmod4_pH10_50ns_2.part0002.edr14900.000 2GH9openmod4_pH10_50ns_3.part0003.edr27800.000 2GH9openmod4_pH10_50ns_4.part0004.edr38800.000 Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Segmentation fault Looking for some hints in the gmx-users list the only thing I found that could be similar to my problem is this old message: http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html What Gromacs version are you using? If it is not 4.5.3, then you're probably running into a bug regarding double precision .edr files that was fixed some time ago. I see in the output error message that the start time for the first two simulations is the same: could be this one the problem for my system? However, I did use tpbconv each time to make restarts of my simulations, I really don't know why the start time is 0.000 in the first two cases. Well, your commands don't agree with the output of eneconv. The names are different. Perhaps you've confused what files you think you're using, or otherwise attempted to append to a file and then gave it a new name. In any case, gmxcheck is your friend here. Is there a problem in the results of simulations if these two simulations have the same start time? Practically, what can I do to concatenate my .edr files? Presumably, yes. As long as the .edr files have no internal corruptions (which, unfortunately, is quite possible if the job frequently went down), then you should be able to concatenate them. That also depends on the version of Gromacs you're using, if you're running into the old bug. It's always helpful to state right up front which version you're using when reporting a problem. -Justin Many thanks in advance and best regards Anna Marabotti Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it mailto:anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man -- 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
[gmx-users] Segmentation Fault in EM
Hi all, I have been running alot of simulations on protein ligand interactions, and my settings/setup/mdp files worked great for one system. Then when we moved to a larger and more complicated system we started getting mdrun segmentation faults during steep energy minimization. This happens on our cluster and on our iMacs. Any help would be appreciated. Also I can attach my mdp files. Thank you TJ Mustard Email: musta...@onid.orst.edu -- 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] Segmentation Fault in EM
TJ Mustard wrote: Hi all, I have been running alot of simulations on protein ligand interactions, and my settings/setup/mdp files worked great for one system. Then when we moved to a larger and more complicated system we started getting mdrun segmentation faults during steep energy minimization. This happens on our cluster and on our iMacs. Any help would be appreciated. Also I can attach my mdp files. There are a whole host of things that could be going wrong. Without substantially more information, including even more (like a thorough description of what these systems are and the exact commands of what worked before), then you won't get any useful advice. -Justin Thank you TJ Mustard Email: musta...@onid.orst.edu -- 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] Segmentation Fault in EM
On January 17, 2011 at 1:20 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: Hi all, I have been running alot of simulations on protein ligand interactions, and my settings/setup/mdp files worked great for one system. Then when we moved to a larger and more complicated system we started getting mdrun segmentation faults during steep energy minimization. This happens on our cluster and on our iMacs. Any help would be appreciated. Also I can attach my mdp files. There are a whole host of things that could be going wrong. Without substantially more information, including even more (like a thorough description of what these systems are and the exact commands of what worked before), then you wont get any useful advice. -Justin Ok, system 1 that worked is biotin and strepavidin in a water box, and the larger system is just rifampicin in a water box for hydration energies. Both ligands are being removed via FEP. As for commands they are identical as we have made a systematic script that sets up our systems. It is: pdb2gmx -f base.pdb -o base.gro -p base.top ===Here we put the ligand .gro and the protein base .gro together. editconf -bt cubic -f base.gro -o base.gro -c -d 3.5 genbox -cp base.gro -cs spc216.gro -o base_b4ion.gro -p base.top grompp -f em.mdp -c base_b4ion.gro -p base.top -o base_b4ion.tpr -maxwarn 2 genion -s base_b4ion.tpr -o base_b4em.gro -neutral -conc 0.01 -pname NA -nname CL -g base_ion.log -p base.top ==Here select SOL grompp -f em.mdp -c base_b4em.gro -p base.top -o base_em.tpr mdrun -v -s base_em.tpr -c base_after_em.gro -g emlog.log -cpo stat_em.cpt ===Segmentation fault occurs here. grompp -f pr.mdp -c base_after_em.gro -p base.top -o base_pr.tpr mdrun -v -s base_pr.tpr -e pr.edr -c base_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt -dhdl dhdl-pr.xvg grompp -f md.mdp -c base_after_pr.gro -p base.top -o base_md.tpr mdrun -v -s base_md.tpr -o base_md.trr -c base_after_md.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dhdl dhdl-md.xvg grompp -f FEP.mdp -c base_after_md.gro -p base.top -o base_fep.tpr mdrun -v -s base_fep.tpr -o base_fep.trr -c base_after_fep.gro -g fep.log -e fep.edr -cpi state_fep.cpt -cpo state_fep.cpt -dhdl dhdl-fep.xvg I can include mdp files if that would help. Thank you, TJ Mustard Thank you TJ Mustard Email: musta...@onid.orst.edu -- 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 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Cant post? Read http://www.gromacs.org/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- 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] Segmentation Fault in EM
TJ Mustard wrote: On January 17, 2011 at 1:20 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: Hi all, I have been running alot of simulations on protein ligand interactions, and my settings/setup/mdp files worked great for one system. Then when we moved to a larger and more complicated system we started getting mdrun segmentation faults during steep energy minimization. This happens on our cluster and on our iMacs. Any help would be appreciated. Also I can attach my mdp files. There are a whole host of things that could be going wrong. Without substantially more information, including even more (like a thorough description of what these systems are and the exact commands of what worked before), then you won't get any useful advice. -Justin Ok, system 1 that worked is biotin and strepavidin in a water box, and the larger system is just rifampicin in a water box for hydration energies. Both ligands are being removed via FEP. As for commands they are identical as we have made a systematic script that sets up our systems. It is: pdb2gmx -f base.pdb -o base.gro -p base.top ===Here we put the ligand .gro and the protein base .gro together. editconf -bt cubic -f base.gro -o base.gro -c -d 3.5 genbox -cp base.gro -cs spc216.gro -o base_b4ion.gro -p base.top grompp -f em.mdp -c base_b4ion.gro -p base.top -o base_b4ion.tpr -maxwarn 2 genion -s base_b4ion.tpr -o base_b4em.gro -neutral -conc 0.01 -pname NA -nname CL -g base_ion.log -p base.top ==Here select SOL grompp -f em.mdp -c base_b4em.gro -p base.top -o base_em.tpr mdrun -v -s base_em.tpr -c base_after_em.gro -g emlog.log -cpo stat_em.cpt ===Segmentation fault occurs here. grompp -f pr.mdp -c base_after_em.gro -p base.top -o base_pr.tpr mdrun -v -s base_pr.tpr -e pr.edr -c base_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt -dhdl dhdl-pr.xvg grompp -f md.mdp -c base_after_pr.gro -p base.top -o base_md.tpr mdrun -v -s base_md.tpr -o base_md.trr -c base_after_md.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dhdl dhdl-md.xvg grompp -f FEP.mdp -c base_after_md.gro -p base.top -o base_fep.tpr mdrun -v -s base_fep.tpr -o base_fep.trr -c base_after_fep.gro -g fep.log -e fep.edr -cpi state_fep.cpt -cpo state_fep.cpt -dhdl dhdl-fep.xvg I can include mdp files if that would help. Yes, please do. -Justin Thank you, TJ Mustard Thank you TJ Mustard Email: musta...@onid.orst.edu -- 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 TJ Mustard Email: musta...@onid.orst.edu -- 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] segmentation fault
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error Back Off! I just backed up md.log to ./#md.log.5# Reading file argon.tpr, VERSION 4.0.7 (single precision) Back Off! I just backed up argon.trr to ./#argon.trr.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# starting mdrun 'Built with Packmol' 100 steps, 1000.0 ps. Segmentation fault there is no error in energy minimization or grommp command. could u please help me? here is my md.out file iin reduced units. cpp = /usr/bin/cpp integrator = md dt = 0.001 nsteps = 100 nstcomm = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 2.9 coulombtype = PME rcoulomb= 2.9 rvdw= 2.9 fourierspacing = 0.35 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ;Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps= GAS ref_t = 2.5 ;generate velocities gen_vel= yes gen_temp= 2.5 gen_seed = 173529 -- 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] segmentation fault
On 15/01/2011 8:50 PM, leila separdar wrote: I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error Back Off! I just backed up md.log to ./#md.log.5# Reading file argon.tpr, VERSION 4.0.7 (single precision) Back Off! I just backed up argon.trr to ./#argon.trr.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# starting mdrun 'Built with Packmol' 100 steps, 1000.0 ps. Segmentation fault What was your command line? What does the end of the logfile say? Why are you using PME for an LJ simulation that presumably has no electrostatic interactions? Mark there is no error in energy minimization or grommp command. could u please help me? here is my md.out file iin reduced units. cpp = /usr/bin/cpp integrator = md dt = 0.001 nsteps = 100 nstcomm = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 2.9 coulombtype = PME rcoulomb= 2.9 rvdw= 2.9 fourierspacing = 0.35 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ;Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps= GAS ref_t = 2.5 ;generate velocities gen_vel= yes gen_temp= 2.5 gen_seed = 173529 -- 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] segmentation fault
I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about this issue?( I have reduced box size, dt, C6=4 , C12=4, mass=1 and temperature. before reducing temperature is 300 and after reducing it is 2.5) On Sun, Jan 16, 2011 at 12:23 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 15/01/2011 8:50 PM, leila separdar wrote: I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error Back Off! I just backed up md.log to ./#md.log.5# Reading file argon.tpr, VERSION 4.0.7 (single precision) Back Off! I just backed up argon.trr to ./#argon.trr.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# starting mdrun 'Built with Packmol' 100 steps, 1000.0 ps. Segmentation fault What was your command line? What does the end of the logfile say? Why are you using PME for an LJ simulation that presumably has no electrostatic interactions? Mark there is no error in energy minimization or grommp command. could u please help me? here is my md.out file iin reduced units. cpp = /usr/bin/cpp integrator = md dt = 0.001 nsteps = 100 nstcomm = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 2.9 coulombtype = PME rcoulomb= 2.9 rvdw= 2.9 fourierspacing = 0.35 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ;Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps= GAS ref_t = 2.5 ;generate velocities gen_vel= yes gen_temp= 2.5 gen_seed = 173529 -- 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] Segmentation fault in g_hbond
Dear gromacs users I used g_hbond tool for hydrogen bond analysis between protein and solvent (water molecules). I have encountered with : Select a group: 3 Selected 3: 'Protein' Select a group: 15 Selected 15: 'SOL' Checking for overlap in atoms between Protein and SOL Calculating hydrogen bonds between Protein (825 atoms) and SOL (22218 atoms) Found 7441 donors and 7654 acceptors Making hbmap structure...done. Reading frame 0 time0.000 Will do grid-seach on 14x14x14 grid, rcut=0.35 Back Off! I just backed up donor.xvg to ./#donor.xvg.2# Reading frame 400 time 1600.000 Found 27249 different hydrogen bonds in trajectory Found 33939 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 1/7441*Segmentation fault* How to fix it? any help will highly appreciated. -- 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] Segmentation fault in g_hbond
Hi, Upgrade to 4.5.x and see if the problem persists. I've hacked g_hbond quite a bit since 4.0.5. Erik leila karami skrev 2010-12-18 14.02: Dear gromacs users I'm using gromacs 4.0.5. with following command: g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn. my system contains protein, dna and water. when I use above command for protein and dna, there is no problem. segmentation fault is only for protein and water. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] Segmentation fault in g_hbond
Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg without segmentation fault. how to file a bugzilla and attach a tpr and xtc/trr? I don't know. size of xtc file is large, how to attach this file to list? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] Segmentation fault in g_hbond
leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg without segmentation fault. I'd like to see the actual output too, although it may not be ncessary if I can reproduce the error myself. how to file a bugzilla and attach a tpr and xtc/trr? I don't know. size of xtc file is large, how to attach this file to list? you could upload it somewhere and post a link to it. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 15.40: leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg without segmentation fault. I'd like to see the actual output too, although it may not be ncessary if I can reproduce the error myself. how to file a bugzilla and attach a tpr and xtc/trr? I don't know. size of xtc file is large, how to attach this file to list? you could upload it somewhere and post a link to it. ..and here's the bugzilla tracker. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] Segmentation fault in g_hbond
leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group I can reproduce the segfault. It doesn't happen without -hbn. I'll have a crack at fixing it. I won't promise to have it done before christmas, but I'll try. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 16.23:
leila karami skrev 2010-12-18 16.18:
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
I can reproduce the segfault. It doesn't happen without -hbn. I'll
have a crack at fixing it. I won't promise to have it done before
christmas, but I'll try.
Fixed it. There's a call to clearPshift in do_merge which causes a
segfault if g_hbond is run without -geminate. Here's what you do:
In gmx_hbond.c, enclose the call in an if-statement:
if (hb-per-pHist)
{
clearPshift((hb-per-pHist[a1][a2]));
}
I'll push this to the master and release branches some time today.
Thanks for reporting this.
Regards,
Erik
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 16.36:
Erik Marklund skrev 2010-12-18 16.23:
leila karami skrev 2010-12-18 16.18:
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
I can reproduce the segfault. It doesn't happen without -hbn. I'll
have a crack at fixing it. I won't promise to have it done before
christmas, but I'll try.
Fixed it. There's a call to clearPshift in do_merge which causes a
segfault if g_hbond is run without -geminate. Here's what you do:
In gmx_hbond.c, enclose the call in an if-statement:
if (hb-per-pHist)
{
clearPshift((hb-per-pHist[a1][a2]));
}
I'll push this to the master and release branches some time today.
Thanks for reporting this.
Regards,
Erik
As it turns out, I (or possibly someone else) had already fixed this
issue in the master and release branches. Hence the solution is again to
update your gromacs installation.
Erik
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] Segmentation fault in g_hbond
Dear Erik there are several hb-per-pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] Segmentation fault in g_hbond
leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb-per-pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group As I said: There's a call to clearPshift in do_merge which causes a segfault. Theres only one call to clearPshift in do_merge as far as I can remember. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 21.15: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb-per-pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? Sorry, forgot to answer this one. I could have a look, but so could you. I would *think* that 4.5.3 is ok in this respect. If you checkout the release-4-5-patches from git.gromacs.org you're definitely safe. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group As I said: There's a call to clearPshift in do_merge which causes a segfault. Theres only one call to clearPshift in do_merge as far as I can remember. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund wrote: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb-per-pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group As I said: There's a call to clearPshift in do_merge which causes a segfault. Theres only one call to clearPshift in do_merge as far as I can remember. There is, and there are no code modifications necessary if the OP simply upgrades to version 4.5.3, which contains the proper code already. -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] Segmentation fault at g_traj
Dear friends:Running several simulations, we have found a problem with the 'g_traj' utility. It doesn't finish properly the files it generates, and gives a segmentation fault. This is what we have done:We are working with double precision. With the file .mdp that is at the end of the mail, we have used 'grompp_d' to generate the .tpr file:grompp_d -maxwarn 1000 -f temp_prueba_mail-list_001_mdpmdp -c ../data/in/pep_ini.gro -r ../data/in/pep_ini.gro -p ../data/in/pep.top -o temp_prueba_mail-list_001_tpr.tprAfter that, we ran the simulation with 'mdrun_d':mdrun_d -s temp_prueba_mail-list_001_tpr.tpr -o temp_prueba_mail-list_001_trr.trr -c ../data/out/gro_unconstr_1.00_01.gro -g ../data/out/log_unconstr_1.00_01.log -e temp_prueba_mail-list_001_edr.edrThen we tried to get the coordinates of the atoms with 'g_traj_d':g_traj_d -f temp_prueba_mail-list_001_trr.trr -s temp_prueba_mail-list_001_tpr.tpr -ox temp_prueba_mail-list_001_ox.xvgAt the terminal, we tell the program to get the coordinates from the group 0 (system), although the error appears also for other groups.Here is where the problem appears. When the program is about to finish, it makes segmentation fault and ends abruptly. The .xvg file has only some of the last lines missing, but those are the lines we are interested in. We have tried different ways: we have used different number of steps, we have get velocities and forces instead of coordinates... and always the same problem appears.We would be very thankful if someone could tell us what is going wrong.Best wishes,Jorge Alberto Jover GaltierUniversidad de Zaragoza, Spain---; VARIOUS PREPROCESSING OPTIONStitle = Yocpp = /usr/bin/cppinclude = define = ; RUN CONTROL PARAMETERSintegrator = md; Start time and timestep in pstinit = 0dt = 0.001000nsteps = 10; For exact run continuation or redoing part of a runinit_step = 0; mode for center of mass motion removalcomm-mode = none; number of steps for center of mass motion removalnstcomm = 1; group(s) for center of mass motion removalcomm-grps = ; OUTPUT CONTROL OPTIONS; Output frequency for coords (x), velocities (v) and forces (f)nstxout = 1nstvout = 1nstfout = 1; Checkpointing helps you continue after crashesnstcheckpoint = 1000; Output frequency for energies to log file and energy filenstlog = 1000nstenergy = 1nstcalcenergy = 1; Output frequency and precision for xtc filenstxtcout = 50xtc-precision = 1000; 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 groupsenergygrps = ; NEIGHBORSEARCHING PARAMETERS; nblist update frequencynstlist = -1; ns algorithm (simple or grid)ns_type = grid; Periodic boundary conditions: xyz (default), no (vacuum); or full (infinite systems only)pbc = no; nblist cut-off rlist = 20domain-decomposition = no; OPTIONS FOR ELECTROSTATICS AND VDW; Method for doing electrostaticscoulombtype = Reaction-Field-zerorcoulomb-switch = 0rcoulomb = 4; Dielectric constant (DC) for cut-off or DC of reaction fieldepsilon-r = 1epsilon-rf = 0; Method for doing Van der Waalsvdw-type = Shift; cut-off lengths rvdw-switch = 0rvdw = 4; Apply long range dispersion corrections for Energy and PressureDispCorr = no; Extension of the potential lookup tables beyond the cut-offtable-extension = 1; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)implicit_solvent = No; OPTIONS FOR WEAK COUPLING ALGORITHMS; Temperature coupling Tcoupl = no; Groups to couple separatelytc-grps = System; Time constant (ps) and reference temperature (K)tau_t = 0.1ref_t = 300; Pressure coupling Pcoupl = noPcoupltype = isotropic; Time constant (ps), compressibility (1/bar) and reference P (bar)tau_p = 1.0compressibility = 4.5e-5ref_p = 1.0; Random seed for Andersen thermostatandersen_seed = 815131; GENERATE VELOCITIES FOR STARTUP RUNgen_vel = yesgen_temp = 300gen_seed = 556380; OPTIONS FOR BONDS constraints = none; Type of constraint algorithmconstraint-algorithm = Shake; Do not constrain the start configurationunconstrained-start = yes; Use successive overrelaxation to reduce the number of shake iterationsShake-SOR = no; Relative tolerance of
Re: [gmx-users] Segmentation fault at g_traj
Jorge Alberto Jover Galtier wrote: Dear friends: Running several simulations, we have found a problem with the 'g_traj' utility. It doesn't finish properly the files it generates, and gives a segmentation fault. This is what we have done: We are working with double precision. With the file .mdp that is at the end of the mail, we have used 'grompp_d' to generate the .tpr file: grompp_d -maxwarn 1000 -f temp_prueba_mail-list_001_mdpmdp -c ../data/in/pep_ini.gro -r ../data/in/pep_ini.gro -p ../data/in/pep.top -o temp_prueba_mail-list_001_tpr.tpr After that, we ran the simulation with 'mdrun_d': mdrun_d -s temp_prueba_mail-list_001_tpr.tpr -o temp_prueba_mail-list_001_trr.trr -c ../data/out/gro_unconstr_1.00_01.gro -g ../data/out/log_unconstr_1.00_01.log -e temp_prueba_mail-list_001_edr.edr Then we tried to get the coordinates of the atoms with 'g_traj_d': g_traj_d -f temp_prueba_mail-list_001_trr.trr -s temp_prueba_mail-list_001_tpr.tpr -ox temp_prueba_mail-list_001_ox.xvg At the terminal, we tell the program to get the coordinates from the group 0 (system), although the error appears also for other groups. Here is where the problem appears. When the program is about to finish, it makes segmentation fault and ends abruptly. The .xvg file has only some of the last lines missing, but those are the lines we are interested in. We have tried different ways: we have used different number of steps, we have get velocities and forces instead of coordinates... and always the same problem appears. We would be very thankful if someone could tell us what is going wrong. You're probably running out of memory. Your .mdp file indicates that you save full-precision coordinates every step (yikes!) over 100,000 steps. If you're trying to print the coordinate of every atom at every time, then the file that g_traj is trying to produce will be enormous, and you'll potentially use up all the memory your machine has. Other diagnostic information that would be useful would be the number of atoms in the system (to see if I'm on to something or completely guessing). Does g_traj work if you just try to output a single frame, or just a few using -b and -e? -Justin Best wishes, Jorge Alberto Jover Galtier Universidad de Zaragoza, Spain --- ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001000 nsteps = 10 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1 nstcalcenergy = 1 ; Output frequency and precision for xtc file nstxtcout= 50 xtc-precision= 1000 ; 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 = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = -1 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist= 20 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field-zero rcoulomb-switch = 0 rcoulomb = 4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 epsilon-rf = 0 ; Method for doing Van der Waals vdw-type = Shift ; cut-off lengths rvdw-switch = 0 rvdw = 4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = no ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t
[gmx-users] Segmentation Fault with g_dielectric
Hello, I am trying to calculate the dielectric constant for pure tetrahydrofuran (THF) at 298K. I keep running into problems though. I have looked through the gmx user list to see if others have had these problems, but I didn't see any mention of them (although I did see that others were asked to report issues with g_dipoles to bugzilla). The first thing I do is run g_dipoles using the command (I do this in order to get the ACF to use in g_dielectric): g_dipoles -f nvt10ns.xtc -s previous.tpr -corr mol -mu 1.75 *I would have liked to attach the tpr and xtc file, but the message was too big. I can send them if they will help* When I do this, I get the following output to terminal: There are 255 molecules in the selection Using volume from topology: 34.3361 nm^3 Last Frame 3 time 12000.001 t0 0, t 12000, teller 30001 **then there is a long pause (approx 5 minutes)** Dipole Moment (Debye) __ Average = 1.9194 Std. Dev. = 0.0085 Error = 0. **Then it lists the different dipole moments, kirkwood factors, and finally an epsilon = 4.47756** (I won't bother to write all of the info down) I wanted to include the output files, but the e-mail was too big and wouldn't go through. I can send them later. It seems that the g_dipoles is working fine for me. Once I have the autocorrelation function (dipcorr.xvg), I want to use g_dielectric. Before I talk about the problems I have here, I wanted to verify a few things about the various options: epsRF - the default here is 78.5, even though the default in g_dipoles is 0 (infinity). I wanted it to be infinity, so I assume I change it. eps0 - this is the epsilon of my liquid - but is it the epsilon that was calculated from g_dipoles (4.47756)? When I run the command: g_dielectric -f dipcorr.xvg -epsRF 0 -d -o -c I get a segmentation fault before anything happens: Read data set containing 2 columns a nd 15001 rows Assuming (from data) that timestep is 0.4, nxtail = 1249 Creating standard deviation numbers ... nbegin = 13, x[nbegin] = 5.2, tbegin = 5 Segmentation Fault If I leave out the -epsRF, I still get the same error. If I include eps0, I still get a segmentation fault. It seems strange to me since GROMACS generates the input and yet has an issue with it. I would like to point out that the manual states to use dipcorr.xvg to get the dielectric constant, but after reading the paper GROMACS references, it seems that Mtot^2 is more appropriate. I tried running the command g_dielectric -f Mtot.xvg, and the segmentation fault went away. Instead lambda went to infinity and there was a fatal error (nparm = 0 in the file ../../../../src/tools/exptfit. c, line 466. I am probably missing something obvious, but I am having a hard time figuring out what it is. I appreciate any help. Thank you for your time, Jenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] segmentation fault in position restrained step
Dear Justin, 1- Could you please check if I have grouped atoms properly? Lastly, I could generate the tpr file for PR step. Since I am getting segmentation fault in the next step I though maybe there is sth wring with charge groups.. However, I have a funda,mental question. I am to compute interaction parameters for ternary system of hexane/polyethylene/ethylene. Sofar I have only hexane as solvent, later polyethylene and ethylene will be added. My questions is for this apolar system, do I need to worry about electrostatic interactions between atoms? I mean could I skip buildig charge groups if I am interested in cacluation of interaction parameters BETWEEN hexane, polyethylene and ethylene? [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18 2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.3 3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.42 4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.54 5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.66 6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.84 7 opls_140 1 HEX H1 1 0.06 1.008 ; qtot -0.78 8 opls_140 1 HEX H2 1 0.06 1.008 ; qtot -0.72 9 opls_140 1 HEX H3 1 0.06 1.008 ; qtot -0.66 10 opls_140 1 HEX H4 2 0.06 1.008 ; qtot -0.6 11 opls_140 1 HEX H5 2 0.06 1.008 ; qtot -0.54 12 opls_140 1 HEX H6 3 0.06 1.008 ; qtot -0.48 13 opls_140 1 HEX H7 3 0.06 1.008 ; qtot -0.42 14 opls_140 1 HEX H8 4 0.06 1.008 ; qtot -0.36 15 opls_140 1 HEX H9 4 0.06 1.008 ; qtot -0.3 16 opls_140 1 HEX H10 5 0.06 1.008 ; qtot -0.24 17 opls_140 1 HEX H11 5 0.06 1.008 ; qtot -0.18 18 opls_140 1 HEX H12 6 0.06 1.008 ; qtot -0.12 19 opls_140 1 HEX H13 6 0.06 1.008 ; qtot -0.06 20 opls_140 1 HEX H14 6 0.06 1.008 ; qtot 0 2- I tried to run the position restrained simulation. VERSION 4.0.7 with mdrun -s Hexane_pr.tpr -o Hexane_pr.tpr -c Hexane_b4md -v output.mdrun_pr. After a few seconds I get segmentation fault error. I did a thorough search on mailing list and found a smilar situation where Mr. MArck Abraham introduced http://oldwiki.gromacs.org/index.php/blowing_=upbut link is not working. Do I need to change the constraint algorithm? Could you please tell me why I am getting segmentation error? Does it have to do with kinetic energy? output.mdrun_pr starting mdrun 'HEX' 500 steps, 1.0 ps. ^Mstep 0 Step 26, time 0.052 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000193, max 0.001508 (between atoms 81 and 100) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2541 2558 31.80.1090 0.1090 0.1090 Step 29, time 0.058 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000200, max 0.001497 (between atoms 1661 and 1678) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 301318 31.40.1091 0.1090 0.1090 1521 1538 30.70.1091 0.1091 0.1090 Step 31, time 0.062 (ps) LINCS WARNING relative constraint deviation after LINCS:rms 0.000184, max 0.001189 (between atoms 1582 and 1596) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 321338 30.40.1091 0.1091 0.1090 1861 1878 31.40.1091 0.1090 0.1090 3481 3498 30.10.1091 0.1091 0.1090 4841 4858 30.30.1091 0.1091 0.1090 Step 33, time 0.066 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000191, max 0.001602 (between atoms 4542 and 4556) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3101 3118 30.50.1091 0.1091 0.1090 Step 38, time 0.076 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000242, max 0.001985 (between atoms 2885 and 2891) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2885 2891 33.20.1090 0.1092 0.1090 Step 39, time 0.078 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000234, max 0.002949 (between atoms 1465 and 1471) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1425
Re: [gmx-users] segmentation fault in position restrained step
Moeed wrote: Dear Justin, 1- Could you please check if I have grouped atoms properly? Lastly, I could generate the tpr file for PR step. Since I am getting segmentation fault in the next step I though maybe there is sth wring with charge groups.. I don't know how your labeling is set up. If your CH3 and CH2 groups are all your charge groups, then you should be fine. In fact, this is what grompp suggested in the note. You can get a sense of what might be appropriate by looking at your force field's .rtp file and looking at the functional groups. However, I have a funda,mental question. I am to compute interaction parameters for ternary system of hexane/polyethylene/ethylene. Sofar I have only hexane as solvent, later polyethylene and ethylene will be added. My questions is for this apolar system, do I need to worry about electrostatic interactions between atoms? I mean could I skip buildig charge groups if I am interested in cacluation of interaction parameters BETWEEN hexane, polyethylene and ethylene? Your atoms have partial charges, do they not? Then you certainly need to consider proper electrostatics treatment. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18 2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.3 3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.42 4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.54 5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.66 6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.84 7 opls_140 1 HEX H1 1 0.06 1.008 ; qtot -0.78 8 opls_140 1 HEX H2 1 0.06 1.008 ; qtot -0.72 9 opls_140 1 HEX H3 1 0.06 1.008 ; qtot -0.66 10 opls_140 1 HEX H4 2 0.06 1.008 ; qtot -0.6 11 opls_140 1 HEX H5 2 0.06 1.008 ; qtot -0.54 12 opls_140 1 HEX H6 3 0.06 1.008 ; qtot -0.48 13 opls_140 1 HEX H7 3 0.06 1.008 ; qtot -0.42 14 opls_140 1 HEX H8 4 0.06 1.008 ; qtot -0.36 15 opls_140 1 HEX H9 4 0.06 1.008 ; qtot -0.3 16 opls_140 1 HEX H10 5 0.06 1.008 ; qtot -0.24 17 opls_140 1 HEX H11 5 0.06 1.008 ; qtot -0.18 18 opls_140 1 HEX H12 6 0.06 1.008 ; qtot -0.12 19 opls_140 1 HEX H13 6 0.06 1.008 ; qtot -0.06 20 opls_140 1 HEX H14 6 0.06 1.008 ; qtot 0 2- I tried to run the position restrained simulation. VERSION 4.0.7 with mdrun -s Hexane_pr.tpr -o Hexane_pr.tpr -c Hexane_b4md -v output.mdrun_pr. After a few seconds I get segmentation fault error. I did a thorough search on mailing list and found a smilar situation where Mr. MArck Abraham introduced http://oldwiki.gromacs.org/index.php/blowing_=up but link is not working. Do I need to change the constraint algorithm? Could you please tell me why I am getting segmentation error? Does it have to do with kinetic energy? Did you do energy minimization? Usually instabilities like this arise because either the system is energetically unstable due to atomic clashes, or something about the underlying model physics is broken. You haven't mentioned how you built your system or if you energy minimized it, so I assume that you simply haven't resolved the clashes in your system. snip define = -DPOSRES If your system is just a box of hexane, restraining anything doesn't make sense to me. One usually employs position restraints on a solute (like a protein) to relax the solvent (usually water) around it. If you're trying to equilibrate a hexane system, you're just wasting your time by restraining any or all of the molecules. -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/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
[gmx-users] Segmentation fault with gromacs executables
Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when I execute, say grompp, I get segmentation fault. But when I use the same command by specifying full path /home/.../gromacs/bin/grompp , it executes without any issues!! Whats wrong going on here? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
