[gmx-users] Help in a thermalization

[Justin Lemkul]

On 3/27/17 4:12 PM, Graziele Bortolini wrote:
> When I tried to do a thermalization for a PSB molecule (it has 66 atoms),
> in vacuum, the molecule rotate around the center of mass. This's my .mdp
> file:
> -------------------
> cpp = /lib/cpp
> integrator = md
> dt = 0.001
> nsteps = 500000
> nstcomm = 1
> nstxout = 0
> nstvout = 0
> nstlog = 0
> nstenergy = 50
> nstxtcout = 50
> energygrps = PSB
> nstlist = 10
> ns_type = grid
> rlist = 0.4
> coulombtype = Cut-off
> optimize_fft = yes
> rcoulomb = 0.8
> vdwtype = shift
> rvdw = 0.8
> 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 = xyz
> -------------------
> So, I tried to put the "comm-mode = angular", it supposedly remove center
> of mass translation and rotation. But when I do it I receive the following
> message:
>
> "WARNING 1 :
>   Removing the rotation around the center of mass in a periodic system,
>   this can lead to artifacts. Only use this on a single (cluster of)
>   molecules. This cluster should not cross periodic boundaries."
>
> What I'm doing wrong?
>

You're not running in vacuo.  By using finite cutoffs and using PBC, you're 
simulating a molecule in some sparsely populated pseudocrystalline state.  To 
run in vacuo, set all cutoffs to zero (which means infinite), use no PBC, and 
set comm-mode = angular.

-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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