[gmx-users] box siz

Justin Lemkul jalemkul at vt.edu
Tue Dec 30 16:39:43 CET 2014

On 12/30/14 5:28 AM, mah maz wrote:
> Dear all,
> I have calculated the size of the box required for my system. however, when
> applying the g_x2top command with this box size, a fatal error occurs:
> 'couldnt find forcefield for all atoms'. making the box larger in size,
> this error is not appeared. what is the exact problem; box size or
> forcefield? and does the larger box affect the simulation parameters?

There's not enough information to say exactly.  Perhaps the original box was too 
small, such that the distances in the .n2t file resulted in too many bonds per 
atom at the edges, perhaps the new box is too large to actually capture the real 
geometry of the system but the .n2t covers up that error by finding what it 
thinks are suitable alternatives.



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


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