[gmx-users] Help in a thermalization

[Graziele Bortolini]

It worked.
Thanks Justin.

2017-03-27 18:23 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 3/27/17 5:17 PM, Graziele Bortolini wrote:
>
>> The error 3 was solved, but when I change to cutoff-scheme = group, I
>> receive:
>>
>> "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:
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>> /2011-June/061989.html
>> 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).
>
> -Justin
>
>
>
>> 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
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
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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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-- 
Att.
G. Bortolini