[gmx-users] Fwd: segmentation fault on gpus
ram bio
rmbio861 at gmail.com
Tue Jun 24 20:06:42 CEST 2014
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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