[gmx-users] error with cut-off length using verlet scheme in stochastic dynamics simulation
Mark Abraham
mark.j.abraham at gmail.com
Wed Sep 28 21:54:22 CEST 2016
Grompp also reports the box volume so check that.
Mark
On Wed, 28 Sep 2016 21:51 Amanda Parker <asparker at ucdavis.edu> wrote:
> It's coming from grompp.
>
> Thank you for your input and quick replies. I will keep working on it.
>
> On Wed, Sep 28, 2016 at 12:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/28/16 3:39 PM, Amanda Parker wrote:
> >
> >> I'm actually using my own potential parameters for use on my own
> >> user-defined atoms, in order to model a simple (haha) coarse-grained
> >> system. What about that could make a difference?
> >>
> >> I did indeed use editconf to create the gro file, and the format looks
> >> identical to others I've used successfully in the past.
> >>
> >> Thanks for pointing out the friction coefficient. My plan is to mess
> with
> >> these parameters once I have it running, but it's good to take note of
> it
> >> now. I also overlooked the coulombtype parameter and will do some
> reading
> >> on that as well. Could this be related to the problem?
> >>
> >>
> > Is the error coming from grompp or mdrun? If it's grompp, I really don't
> > know what's causing it. If it's from mdrun, yes, it means your physical
> > model is unstable and it's probably due to bad settings or topology.
> >
> > -Justin
> >
> >
> > Amanda
> >>
> >> On Wed, Sep 28, 2016 at 12:24 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >>
> >>
> >>>
> >>> On 9/28/16 3:20 PM, Amanda Parker wrote:
> >>>
> >>> Thank you for your reply! I did not realize that rcoulomb and rvdw were
> >>>> relevant and will look into them. Below is the full text of my mdp
> file:
> >>>>
> >>>>
> >>>>
> >>>> ; RUN CONTROL PARAMETERS
> >>>> integrator = sd ; Stochastic Langevin dynamics
> >>>> ; Start time and timestep in ps
> >>>> tinit = 0
> >>>> dt = 0.02
> >>>> nsteps = 1000000 ;
> >>>> ; For exact run continuation or redoing part of a run
> >>>> init_step = 0
> >>>> ; Part index is updated automatically on checkpointing (keeps files
> >>>> separate)
> >>>> simulation_part = 1
> >>>> ; mode for center of mass motion removal
> >>>> comm-mode = Linear
> >>>> ; number of steps for center of mass motion removal
> >>>> nstcomm = 100
> >>>> ; group(s) for center of mass motion removal
> >>>> comm-grps = system
> >>>>
> >>>> ; LANGEVIN DYNAMICS OPTIONS
> >>>> ; Friction coefficient (amu/ps) and random seed
> >>>> bd_fric = 0
> >>>> ld_seed = 1735
> >>>> ; Groups to couple separately
> >>>> tc_grps = system
> >>>> ; Time constant (ps) and reference temperature (K)
> >>>> tau_t = 0.02
> >>>>
> >>>>
> >>> Your system is going to be very overdamped. Remember that tau-t is a
> >>> friction coefficient when using sd, so it's in ps^-1.
> >>>
> >>> ref_t = 300
> >>>
> >>>>
> >>>> ; OUTPUT CONTROL OPTIONS
> >>>> ; Output frequency for coords (x), velocities (v) and forces (f)
> >>>> nstxout = 0
> >>>> nstvout = 0
> >>>> nstfout = 0
> >>>> ; Output frequency for energies to log file and energy file
> >>>> nstlog = 10000
> >>>> nstcalcenergy = 10000
> >>>> nstenergy = 10000
> >>>> ; Output frequency and precision for .xtc file
> >>>> nstxtcout = 10000
> >>>> xtc-precision = 1000
> >>>> ; This selects the subset of atoms for the .xtc file. You can
> >>>> ; select multiple groups. By default all atoms will be written.
> >>>> xtc-grps =
> >>>> ; Selection of energy groups
> >>>> energygrps =
> >>>>
> >>>>
> >>>> nstlist = 10
> >>>> ns_type = grid
> >>>> rlist = 2.0
> >>>> rcoulomb = 2.0
> >>>> rvdw = 2.0
> >>>>
> >>>>
> >>>> What force field uses 2.0-nm cutoffs? This certainly shouldn't
> trigger
> >>> the error you mentioned before with a huge box, so something else is
> >>> going
> >>> on. You're sure that the box vectors are in the right format in the
> .gro
> >>> file? You used editconf rather than editing them manually, or you
> >>> correctly preserved the format in the latter case?
> >>>
> >>> ; PME electrostatics parameters
> >>>
> >>>> cutoff-scheme = Verlet
> >>>> coulombtype = Cut-off
> >>>>
> >>>>
> >>> A plain cutoff is going to induce horrible artifacts...
> >>>
> >>> -Justin
> >>>
> >>>
> >>> pbc = xyz
> >>>
> >>>>
> >>>> On Wed, Sep 28, 2016 at 12:15 PM, Justin Lemkul <jalemkul at vt.edu>
> >>>> wrote:
> >>>>
> >>>>
> >>>>
> >>>>> On 9/28/16 3:12 PM, Amanda Parker wrote:
> >>>>>
> >>>>> Hello,
> >>>>>
> >>>>>>
> >>>>>> I am trying to run a stochastic dynamics simulation and am getting
> the
> >>>>>> error:
> >>>>>>
> >>>>>> "The cut-off length is longer than half the shortest box vector or
> >>>>>> longer than the smallest box diagonal element. Increase the box
> size
> >>>>>> or
> >>>>>> decrease rlist."
> >>>>>>
> >>>>>> I've increased my box vectors to 100 nm, 100 nm, 100 nm (as I see
> >>>>>> confirmed
> >>>>>> at the bottom of my .gro file). I am using the Verlet cut-off
> scheme,
> >>>>>> which
> >>>>>> as I understand it makes rlist irrelevant and uses its own default
> >>>>>> cut-off
> >>>>>> length (perhaps of 0.005?), unless I specify
> verlet-buffer-tolerance =
> >>>>>> -1.
> >>>>>> I have tried using no verlet-buffer-tolerance line, as well as using
> >>>>>> verlet-buffer-tolerance = -1 and setting rlist = 2. Both of these
> >>>>>> options
> >>>>>> continue to give the error above.
> >>>>>>
> >>>>>> How do I check the cut-off length for Verlet scheme? Without being
> >>>>>> able
> >>>>>> to
> >>>>>> do that, I cannot confirm that the cut-off length is indeed longer
> >>>>>> than
> >>>>>> half the shortest box vector. That said, I would be surprised if the
> >>>>>> cut-off length was longer than 50 nm.
> >>>>>>
> >>>>>> I'm happy to include copies of any files that you feel are necessary
> >>>>>> to
> >>>>>> understanding this problem. At this point it seems the only
> >>>>>> information
> >>>>>> necessary are the box vectors and cut-off length (and in this case
> the
> >>>>>> fact
> >>>>>> that I'm using Verlet), but I may be wrong.
> >>>>>>
> >>>>>> Any insight is much appreciated.
> >>>>>>
> >>>>>>
> >>>>>> Post the full text of your .mdp file. rlist isn't the only cutoff
> >>>>>> that
> >>>>>>
> >>>>> matters. rcoulomb and rvdw can trigger the problem, too. There's
> >>>>> clearly
> >>>>> something weird going on.
> >>>>>
> >>>>> -Justin
> >>>>>
> >>>>> --
> >>>>> ==================================================
> >>>>>
> >>>>> 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
> >>>>>
> >>>>> ==================================================
> >>>>> --
> >>>>> Gromacs Users mailing list
> >>>>>
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> 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
> >>>
> >>> ==================================================
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/Support
> >>> /Mailing_Lists/GMX-Users_List before posting!
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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 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
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> > * Please search the archive at http://www.gromacs.org/Support
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