[gmx-users] error with cut-off length using verlet scheme in stochastic dynamics simulation
Amanda Parker
asparker at ucdavis.edu
Wed Sep 28 21:51:11 CEST 2016
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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>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> 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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>>>
> --
> ==================================================
>
> 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
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>
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