[gmx-users] error with cut-off length using verlet scheme in stochastic dynamics simulation
Justin Lemkul
jalemkul at vt.edu
Wed Sep 28 21:47:54 CEST 2016
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
>>>>
>>>> * 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
>>
>> ==================================================
>> --
>> 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
==================================================
More information about the gromacs.org_gmx-users
mailing list