Sub: Segmentation fault Dear Justin and Vivek,
I came to know what was my fault. I added the refcoordscale = com in .mdp file and it going fine. I have through the many references for refcoordscale, despite of some information I am not getting what exactly it is? Kindly give me some hit. Surya Graduate student India. On Sun, Aug 28, 2016 at 3:30 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: Segmentation fault (Justin Lemkul) > 2. gmx: malloc(): memory corruption (Quyen V. Vu) > 3. KALP-15 tutorial (Roshan Shrestha) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 27 Aug 2016 22:17:13 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Segmentation fault > Message-ID: <960b62bc-d72d-9ad7-4625-e2c279df5...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 8/27/16 5:32 PM, vivek naik wrote: > > I don't think you can do a simulation with pressure if you have position > > restraints, except if your restrained atoms are all in the same plane. > > This is not true. > > > However, ref_coordscaling option should be 'com', which should make it > > better than it is now. > > > > "com" is just one possible option, but it is probably the most stable in > most cases. > > > Also, there is no way isotropic pressure is going to work. it has to be > > anisotropic (xy and z, with the first one being kept to zero). > > > > Anisotropic means all box vectors can vary independently and is usually > applied > to crystals or other solid materials. Coupling xy and z separately is > semiisotropic and is usually used with membranes and surfaces. For a > simple > aqueous protein system, isotropic is in fact correct. > > -Justin > > > Vivek > > > > On Sat, Aug 27, 2016 at 12:15 PM, Seera Suryanarayana < > paluso...@gmail.com> > > wrote: > > > >> Dear gromacs users, > >> > >> I have done mdrun for 10ns with position restrain of interest of our > >> residues. Here I woulk like to explain how I did the position restrain. > >> > >> During gmx pdb2gmx command we usually get posre.itp file which we use in > >> the equilibrium process to restraint the protein. As I want to do real > >> mdrun with restraint on some residues, I just edited the posre.itp file > and > >> kept the restrain information only for residues of my interest and I > define > >> in the md.mdp file as "define =_DPOSRES ; position restrain the > >> protein". I haven't anything to the topology file. When I executed the > >> grompp command I got following warning and then error. > >> > >> WARNING 1 [file md.mdp]: > >> you are using pressure coupling with absolute positions restraints, this > >> will give artifacts. use the refcoord_scaling option and the error was > too > >> many wanrings[1], gmx terminated. Then I executed grompp with the > -maxwarn > >> 1. After preprocessing I did simuations for 10ns. When I try to remove > the > >> PBC with trjconv command I got segmentaion fault error. I request you to > >> tell me What I did wrong and how to resolve it? > >> > >> Thanks in advance > >> Surya > >> Graduate student > >> India. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at http://www.gromacs.org/ > >> Support/Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > Message: 2 > Date: Sun, 28 Aug 2016 14:47:30 +0700 > From: "Quyen V. Vu" <vuqv.p...@gmail.com> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] gmx: malloc(): memory corruption > Message-ID: > <CA+CKAfwj34UDR5kAT_3M+cvOG8QE+YowGYsOXrNYUjsQh+q3hg@ > mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear GMX user, > I have just installed *gromacs 2016.1* on my machine and run mdrun with > these option: > ------------------------------------------------------------ > ------------------------------------- > title = 50AT DNA MD simulation > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 5000 ; 2 * 5000000 = 10000 ps > (10 ns) > dt = 0.002 ; 2 fs > ; Output control > nstxout = 500 ; save coordinates every > 20.0 ps > nstvout = 500 ; save velocities every > 20.0 ps > nstenergy = 500 ; save energies every 20.0 > ps > nstlog = 500 ; update log file every > 20.0 ps > nstxout-compressed = 500 ; save compressed > coordinates every 20.0 ps > ; nstxout-compressed replaces nstxtcout > compressed-x-grps = SYSTEM ; replaces xtc-grps > ; 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 > cutoff-scheme = Verlet > ns_type = grid ; search neighboring grid > cells > nstlist = 40 ; 20 fs, largerly > irrelevant with Verlet scheme > rcoulomb = 1.0 ; short-range electrostatic > cutoff (in nm) > rvdw = 1.0 ; short-range van der Waals > cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for > long-range electrostatics > pme_order =5 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = Nose-Hoover ; More accurate thermostat > nsttcouple = 1 > tc-grps = DNA SOL ION ; three coupling groups - > more accurate > tau_t = 0.1 0.1 0.1 ; time constant, in ps > ref_t = 298 298 298 ; 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 ;do not generate Velocity > ------------------------------------------------------------ > ------------------------------------- > *After that, I use trjconv to get position of DNA by command:* > gmx trjconv -s md.tpr -f md.xtc -o md_mol.xtc -pbc mol -ur compact > and gmx prompt: > Group 0 ( System) has 500179 elements > Group 1 ( DNA) has 3198 elements > Group 2 ( NA) has 129 elements > Group 3 ( CL) has 31 elements > Group 4 ( Water) has 496821 elements > Group 5 ( SOL) has 496821 elements > Group 6 ( non-Water) has 3358 elements > Group 7 ( Ion) has 160 elements > Group 8 ( NA) has 129 elements > Group 9 ( CL) has 31 elements > Group 10 ( Water_and_ions) has 496981 elements > > *I type 1 and press Enter then get message:* > Select a group: 1 > Selected 1: 'DNA' > Reading frame 0 time 0.000 > Precision of md.xtc is 0.001 (nm) > Using output precision of 0.001 (nm) > > Back Off! I just backed up md_mol.xtc to ./#md_mol.xtc.2# > *** Error in `gmx': malloc(): memory corruption: 0x0000000001be5c30 *** > Aborted > > > *Could you tell me this error is caused by me or gromacs program?* > *Thank you* > > > ------------------------------ > > Message: 3 > Date: Sun, 28 Aug 2016 15:34:34 +0545 > From: Roshan Shrestha <roshan...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] KALP-15 tutorial > Message-ID: > <CAGE0GtTMw9hJ7smvKHUWzRUKdKes=6wKfQZHu07Y05BaGi26AQ@mail. > gmail.com> > Content-Type: text/plain; charset=UTF-8 > > After using this step- > *perl inflategro.pl <http://inflategro.pl> system.gro 4 DPPC 14 > system_inflated.gro 5 area.dat* > Reading..... > Scaling lipids.... > There are 128 lipids... > with 50 atoms per lipid.. > > Determining upper and lower leaflet... > 64 lipids in the upper... > 64 lipids in the lower leaflet > > Centering protein.... > Checking for overlap.... > ...this might actually take a while.... > 100 % done... > There are 2 lipids within cut-off range... > 1 will be removed from the upper leaflet... > 1 will be removed from the lower leaflet... > > Writing scaled bilayer & centered protein... > > > Calculating Area per lipid... > Protein X-min/max: 26 40 > Protein Y-min/max: 25 39 > X-range: 14 A Y-range: 14 A > Building 14 X 14 2D grid on protein coordinates... > Calculating area occupied by protein.. > full TMD.. > upper TMD.... > lower TMD.... > Area per protein: 2 nm^2 > Area per lipid: 10.4716089904762 nm^2 > > Area per protein, upper half: 1.75 nm^2 > Area per lipid, upper leaflet : 10.4755772444444 nm^2 > > Area per protein, lower half: 2 nm^2 > Area per lipid, lower leaflet : 10.4716089904762 nm^2 > > Writing Area per lipid... > Then I updated [ molecules] section of my topol.top as > [ molecules ] > ; Compound #mols > DPPC 126 > Protein 1 > Then I ran energy minimization. After that I used > *perl inflategro.pl <http://inflategro.pl> EM.gro 0.95 DPPC 0 > system_shrink1.gro 5 area_shrink1.dat* > I got, > Reading..... > Scaling lipids.... > There are 128 lipids... > with 50 atoms per lipid.. > > Determining upper and lower leaflet... > 64 lipids in the upper... > 64 lipids in the lower leaflet > > No protein coordinates found... > Writing scaled bilayer & centered protein... > > > Calculating Area per lipid... > Protein X-min/max: 10000 -9999 > Protein Y-min/max: 10000 -9999 > X-range: -19999 A Y-range: -19999 A > Building -19999 X -19999 2D grid on protein coordinates... > Calculating area occupied by protein.. > full TMD.. > upper TMD.. > lower TMD.. > Area per protein: 0 nm^2 > Area per lipid: 0.583197761890625 nm^2 > > Area per protein, upper half: 0 nm^2 > Area per lipid, upper leaflet : 0.583197761890625 nm^2 > > Area per protein, lower half: 0 nm^2 > Area per lipid, lower leaflet : 0.583197761890625 nm^2 > > Writing Area per lipid... > Done! > > *Clearly there is some mistake in here as the Area per protein is 0 and > area per lipid is very low compared to the experimental value.* > > > -- > Roshan Shrestha > Graduate Student > Central Department of Physics,Tribhuvan University > Kathmandu,Nepal > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 148, Issue 102 > ******************************************************* > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.