[gmx-users] Help in a thermalization

[Graziele Bortolini]

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.


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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-- 
Att.
G. Bortolini