[gmx-users] Segmentation fault after warning regarding Listed nonbonded interaction
Justin Lemkul
jalemkul at vt.edu
Thu Jul 17 19:24:33 CEST 2014
On 7/17/14, 1:18 PM, Alexandre Barrozo wrote:
> Hey Vivek,
>
>
> Thanks for the suggestion. I tried this, but I still get the same problem.
>
Reducing the timestep is just a band-aid for the underlying problems. Sometimes
it can be useful in initial preparation for very sensitive systems, but in this
case I think it is clear that the topology is not sane.
-Justin
>
> Cheers,
>
> Alex
>
>
> 2014-07-17 17:58 GMT+02:00 vivek sinha <viveksinha20002 at gmail.com>:
>
>> Hey Alex,
>> I was also having the same error from two days although my topology files
>> and mdp files were (I think) correct. Just two hours ago I corrected the
>> problem. I just changed the timestep from 0.002 to 0.0002 and it worked.
>> You can also try this.
>>
>> Regards,
>> Vivek Sinha
>>
>>
>> On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo <barrozo.ah at gmail.com>
>> wrote:
>>
>>> Hi everybody,
>>>
>>>
>>> I am trying to make a simulation of an enzyme containing a metal ion
>> using
>>> a dummy model for it. I have inserted all the parameters, generated the
>>> topology, solvated the system, without any problem.
>>>
>>> When I try to run a first equilibration, I get the following warning:
>>>
>>>
>>>
>>> WARNING: Listed nonbonded interaction between particles 127 and 134*
>>> at distance 3f which is larger than the table limit 3f nm.
>>>
>>> This is likely either a 1,4 interaction, or a listed interaction inside
>>> a smaller molecule you are decoupling during a free energy calculation.
>>> Since interactions at distances beyond the table cannot be computed,
>>> they are skipped until they are inside the table limit again. You will
>>> only see this message once, even if it occurs for several interactions.
>>>
>>> *These particles are close to the dummy model for the metal. I believe
>> the
>>> problem might be related to that, but I had no problem in generating
>>> topologies, or anything like that.
>>>
>>>
>>> After that warning, I have a Segmentation fault.
>>>
>>>
>>> Here is my mdp file for the test equilibration that I was trying:
>>>
>>> define = -DPOSRES -DPOSRES_WATER ; position
>> restrain
>>> the protein
>>> ; Run parameters
>>> integrator = md ; leap-frog
>>> integrator
>>> nsteps = 50000 ; 2 * 50000 = 100
>>> ps
>>> dt = 0.001 ; 1 fs
>>> ; Output control
>>> nstxout = 500 ; save
>> coordinates
>>> every 1.0 ps
>>> nstvout = 500 ; save velocities
>>> every 1.0 ps
>>> nstenergy = 500 ; save energies
>>> every 1.0 ps
>>> nstlog = 500 ; update log file
>>> every 1.0 ps
>>> ; Bond parameters
>>> continuation = no ; first dynamics
>>> run
>>> ; constraint_algorithm = lincs ; holonomic
>>> constraints
>>> constraints = none ; all bonds (even
>>> heavy atom-H bonds) constrained
>>> ; Neighborsearching
>>> cutoff-scheme = Verlet
>>> ns_type = grid ; search
>>> neighboring grid cells
>>> nstlist = 30 ; 20 fs, largely
>>> irrelevant with Verlet
>>> rcoulomb = 1.0 ; short-range
>>> electrostatic cutoff (in nm)
>>> rvdw = 1.0 ; short-range van
>>> der Waals cutoff (in nm)
>>> ; Electrostatics
>>> coulombtype = PME ; Particle Mesh
>>> Ewald for long-range electrostatics
>>> pme_order = 4 ; cubic
>>> interpolation
>>> fourierspacing = 0.16 ; grid spacing
>> for
>>> FFT
>>> ; Temperature coupling is on
>>> tcoupl = V-rescale ; modified
>>> Berendsen thermostat
>>> tc-grps = Protein Non-Protein ; two coupling
>>> groups - more accurate
>>> tau_t = 0.1 0.1 ; time constant,
>> in
>>> ps
>>> ref_t = 1 1 ; reference
>>> temperature, one for each group, in K
>>> ; Pressure coupling is off
>>> pcoupl = no ; no pressure
>>> coupling in NVT
>>> ; Periodic boundary conditions
>>> pbc = xyz ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr = EnerPres ; account for
>>> cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel = yes ; assign
>> velocities
>>> from Maxwell distribution
>>> gen_temp = 1 ; temperature for
>>> Maxwell distribution
>>> gen_seed = -1 ; generate a
>> random
>>> seed
>>>
>>>
>>>
>>> Any clue about what is going on?
>>>
>>>
>>> Cheers,
>>>
>>> Alex
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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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