[gmx-users] Vacuum simulation in GMX 5

[Mark Abraham]

On Wed, May 6, 2015 at 7:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Please don't reply to the entire digest, and please remember to change the
> subject line.
>
> On 5/6/15 1:13 PM, Eudes Fileti wrote:
>
> > ; Neighborsearching and short-range nonbonded interactions
> > cutoff-scheme            = verlet
> > nstlist                  = 20
> > ns_type                  = grid
> > pbc                      = xyz
> > rlist                    = 1.2
> > ; Electrostatics
> > coulombtype              = cut-off
> > rcoulomb                 = 1.2
> > ; van der Waals
> > vdwtype                  = cutoff
> > vdw-modifier             = force-switch
> > rvdw-switch              = 1.0
> > rvdw                     = 1.2
>
> This input file clearly isn't what you described before, because here
> you're
> using PBC and finite cutoffs.
>
> A plain cutoff for electrostatics with a finite cutoff will be very
> inaccurate.
>
>  > couple-moltype           = Pept      ; name of moleculet ype to decouple
>
> Does this mean you're decoupling a protein (pept = peptide?).  If so, that
> will
> be unavoidably slow, even for short peptides.  It also isn't likely to
> converge
> very well.
>
> Running a single molecule in gas phase (which was the original question) is
> straightforward:
>
> nstlist         = 0
> ns_type         = grid  ; simple also works, doesn't seem relevant
> rlist           = 0
> cutoff-scheme   = group
> vdwtype         = cutoff
> rvdw            = 0
> coulombtype     = cutoff
> rcoulomb        = 0
> pbc             = no
>

... and if that is slow, that would be a perfectly good reason to run it in
GROMACS 4.6.7. (Better support for this kind of calc is underway, but not
for GROMACS 5.1)

Mark

-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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