[gmx-users] Gigantic boxes

[Justin Lemkul]

On 6/23/17 6:20 AM, Sergio Manzetti wrote:
> Hi, I Have prepared a box, which just grows beyond proportions in order to satisfy grompp complaining about the box being less than the double of rlist, so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box quickly becomes over 14x14x14. When one visualizes it one can see that the molecule is surrounded by at least 5 Å of waters in all directions, so there is plenty of water in the system. Nevertheless, grompp wants even bigger box, and thus more water.
> 
> Is this common in MD simulations to run megaboxes for molecules that are virtually disappearing in the large water molecule number?
> 

No, it's not.  Make sure you're specifying your cutoffs in nm, not A.

-Justin

-- 
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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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