[gmx-users] Help in a thermalization
jalemkul at vt.edu
Mon Mar 27 23:24:06 CEST 2017
On 3/27/17 5:17 PM, Graziele Bortolini wrote:
> The error 3 was solved, but when I change to cutoff-scheme = group, I
> "Fatal error:
> The largest charge group contains 66 atoms. The maximum is 32."
> I've tried to make this before, and I saw your answer about this error in
> this link:
> But I don't understand what I need to do.
Apparently your whole molecule is assigned to a single charge group, which is
not supported. In this specific case (infinite cutoffs), charge groups are
irrelevant, but in general the idea is that chemical moieties are assigned to
groups of integral charge (e.g. -CH3, -NH2, -CH2OH, etc). See the parent force
field for examples. Some (most) force fields do not use charge groups at all,
so you can just assign every atom to its own charge group and not worry about it
(again, because your nonbonded setup doesn't depend on it).
> 2017-03-27 17:56 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>> On 3/27/17 4:50 PM, Graziele Bortolini wrote:
>>> I do it too, my .mdp file now is like :
>>> cpp = /lib/cpp
>>> integrator = md
>>> dt = 0.001
>>> nsteps = 500000
>>> nstcomm = 1
>>> comm-mode = angular
>>> nstxout = 0
>>> nstvout = 0
>>> nstlog = 0
>>> nstenergy = 50
>>> nstxtcout = 50
>>> energygrps = PSB
>>> nstlist = 10
>>> ns_type = grid
>>> rlist = 0
>>> coulombtype = Cut-off
>>> optimize_fft = yes
>>> rcoulomb = 0
>>> vdwtype = shift
>>> rvdw = 0
>>> tcoupl = berendsen
>>> tc_grps = system
>>> ref_t = 300.0
>>> tau_t = 0.1
>>> pcoupl = berendsen
>>> ref_p = 1.000
>>> compressibility = 4.5e-5
>>> tau_p = 1.0
>>> pcoupltype = isotropic
>>> gen_vel = yes
>>> gen_temp = 300.0
>>> pbc = no
>>> but I receive another errors messages:
>>> ERROR 1 [file teste2.mdp]:
>>> With Verlet lists only full pbc or pbc=xy with walls is supported
>>> ERROR 2 [file teste2.mdp]:
>>> The box volume is required for calculating rlist from the energy drift
>>> with verlet-buffer-tolerance > 0. You are using at least one unbounded
>>> dimension, so no volume can be computed. Either use a finite box, or set
>>> rlist yourself together with verlet-buffer-tolerance = -1.
>> Both of these are solved with cutoff-scheme = group.
>> ERROR 3 [file teste2.mdp]:
>>> With switched vdw forces or potentials, rvdw-switch must be < rvdw
>> You have an infinite cutoff, there's nothing to switch or shift. You need
>> vdwtype = cutoff.
>> 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
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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
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