[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
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
