[gmx-users] Fwd: segmentation fault on gpus
Mark Abraham
mark.j.abraham at gmail.com
Wed Jun 25 07:57:05 CEST 2014
In the Verlet scheme, mdrun will change rlist to conserve energy and
maximize performance. Just leave it alone.
Mark
On Jun 24, 2014 10:18 PM, "ram bio" <rmbio861 at gmail.com> wrote:
> so, is it that rlist should be less than rc?
>
>
> On Tue, Jun 24, 2014 at 12:42 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
> > On Tue, Jun 24, 2014 at 7:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > >
> > > On 6/24/14, 12:14 PM, ram bio wrote:
> > >>
> > >> hi Justin,
> > >>
> > >> Thanks, that makes sense, however I was able to use the same ligand
> > >> toplogy
> > >> files with earlier versions like gromacs 4.5.4 to simulate protein
> > ligand
> > >> complexes. I can simulate protein-ligand complexes with the current
> > >> versions also but only for the crystal structures that have ligand
> bound
> > >> to
> > >> it, not the modelled proteins with ligands bound.
> > >>
> > >
> > > So the same ligand works elsewhere, but not in a specific complex?
> That
> > > implicates the starting structure or the quality of the protein
> > structure.
> > > Other notes below.
> > >
> > >
> > >> and also I would appreciate any comments on the mdp file as below:
> > >>
> > >> title = Bilayer-500
> > >> cpp = /lib/cpp
> > >> constraint_algorithm = lincs
> > >> constraints = all-bonds; added
> > >> lincs_iter = 1; added
> > >> lincs_order = 4; added
> > >> integrator = md;
> > >> dt = 0.002
> > >> tinit = 0;
> > >> nsteps = 1000000 ; 2 ns
> > >> nstcomm = 500
> > >> nstxout = 5000
> > >> nstvout = 5000
> > >> nstfout = 0
> > >> nstxtcout = 500
> > >> xtc_precision = 1000
> > >> nstlog = 500
> > >> nstenergy = 500
> > >> nstlist = 50
> > >
> > >
> > > This may work well in terms of GPU performance, but could be
> problematic
> > if
> > > there are very sensitive cases.
> >
> > Why would it be problematic?
> >
> > >
> > >> ns_type = grid; added
> > >> nstcalclr = 1
> > >> ; long range interactions
> > >> coulombtype = PME
> > >> rlist = 1.4
> > >> rcoulomb = 1.2
> > >> rvdw = 1.2
> >
> > Setting rlist != rc doesn't make sense for the Verlet scheme.
> >
> > >> fourierspacing = 0.16
> > >> pme_order = 4
> > >> vdw-type = Cut-off
> > >> cutoff-scheme = Verlet
> > >> Tcoupl = v-rescale
> > >> tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1
> > >> 0.1
> > >> tc-grps = Protein POP SOL NA CL LIG SOD CLA
> > >> ref_t = 303 303 303 303 303 303 303 303
> > >
> > >
> > > This tc-grp setup is total nonsense.
> > >
> > > http://www.gromacs.org/Documentation/Terminology/Thermostats
> > >
> > > -Justin
> > >
> > >
> > >> ; Energy monitoring
> > >> energygrps = Protein POP SOL SOD CLA LIG NA CL
> > >> Pcoupl = Berendsen
> > >> pcoupltype = semiisotropic
> > >> tau_p = 1.0 1.0
> > >> compressibility = 4.5e-5 4.5e-5
> > >> ref_p = 1.0 1.0
> > >> DispCorr = no ; added
> > >> ;generate velocites is on at 293K
> > >> gen_vel = yes
> > >> gen_temp = 303.0
> > >> gen_seed = 478905
> > >> comm-mode = Linear
> > >> comm-grps = System
> > >>
> > >> Thanks,
> > >> Pramod
> > >>
> > >>
> > >>
> > >>
> > >> On Mon, Jun 23, 2014 at 8:03 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >>
> > >>>
> > >>>
> > >>> On 6/23/14, 5:53 PM, ram bio wrote:
> > >>>
> > >>>> Dear Gromacs Users,
> > >>>>
> > >>>> I have been trying to simulate protein-ligand complex using gromacs
> > >>>> versions that use verlet cutoff scheme on gpus.
> > >>>>
> > >>>> These are some of the issues that i could resolve, and any kind of
> > >>>> suggestion or help is appreciated.
> > >>>>
> > >>>> 1. With gromacs 4.6.5 i could simulate crystal structure from pdb
> but
> > >>>> not
> > >>>> modelled protein with ligand always ended up in segmentation fault.
> > The
> > >>>> MD
> > >>>> run during equillibration runs for gew thousands of steps and errors
> > out
> > >>>> as
> > >>>> segmentation fault, so i have to rerun using previous cpt file, for
> a
> > >>>> run
> > >>>> of 2ns to complete i have to rerun it for 7-10 times.
> > >>>>
> > >>>> So if the the system id not minimized, why would it go into rerun?
> > >>>>
> > >>>> 2. I though it could be a bug and used 4.6.3 and 5.0 release, with
> > this
> > >>>> trial i could equillibrate just modelled protein but not with the
> > >>>> protein-ligand complex. The same error occurs as i mentioned above
> > with
> > >>>> protein-ligand complex...
> > >>>>
> > >>>> I am attaching my mdp file and the minimized structure that i am
> using
> > >>>> for
> > >>>> equillibration.
> > >>>>
> > >>>>
> > >>> The list doesn't accept attachments.
> > >>>
> > >>> It seems clear to me that your ligand topology is not stable. If the
> > >>> protein works, but the protein+ligand doesn't, what's changing?
> That's
> > >>> the
> > >>> likeliest source of your problem.
> > >>>
> > >>> -Justin
> > >>>
> > >>> --
> > >>> ==================================================
> > >>>
> > >>> Justin A. Lemkul, Ph.D.
> > >>> Ruth L. Kirschstein NRSA 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
> > >>>
> > >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > >>> http://mackerell.umaryland.edu/~jalemkul
> > >>>
> > >>> ==================================================
> > >>> --
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> > >>>
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA 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
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
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