[gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

[Justin Lemkul]

On 3/16/16 3:02 PM, Poncho Arvayo Zatarain wrote:
> Hello, due to one of my last question and about the error:  The cut-off
> length is longer than half the shortest box vector or longer than the
> smallest box diagonal element. Increase the box size or decrease rlist. How
> can do large the box? My .gro files vectors are 8.90000 8.900000 and 7.900000
> and my cutoff lenghts are: nstlist = 10 ; 10 fsrlist	= 1.2 ; short-range
> neighborlist cutoff (in nm)rcoulomb	= 1.2 ; short-range electrostatic cutoff
> (in nm)rvdw = 1.2 ; short-range van der Waals cutoff (in nm)vdwtype = cutoff
>

A box of that size, in concert with those cutoffs, should not generate that 
warning unless the system is blowing up (or in this case, collapsing, but same 
problem).

-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

==================================================