[gmx-users] Help in a thermalization

[Justin Lemkul]

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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