[gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 102
Seera Suryanarayana
palusoori at gmail.com
Mon Aug 29 12:17:01 CEST 2016
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-request at maillist.sys.kth.se> wrote:
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> 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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Segmentation fault
> Message-ID: <960b62bc-d72d-9ad7-4625-e2c279df56a5 at 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 <
> palusoori at 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-request at 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
>
> jalemkul at 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.phys at gmail.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at 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 <roshanpra at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] KALP-15 tutorial
> Message-ID:
> <CAGE0GtTMw9hJ7smvKHUWzRUKdKes=6wKfQZHu07Y05BaGi26AQ at 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
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