[gmx-users] Vacuum simulation in GMX 5

[Justin Lemkul]

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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

-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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