[gmx-users] Non-Integral Charges

[Justin Lemkul]

On 1/12/16 8:54 AM, sun wrote:
> Hello Everyone I want to know how to change the non-integral charges? I am
> simulating a pentameric model of protein in water and the net charge comes
> out to be -5.0. Everything goes ok till final mdrun. As soon as its started,
> it carshes. Is it dus to wring topology as the charges are non-integral?

-5 is an integral charge. Typically one does not do simulations with a *net* 
charge, though.  But the charge alone will not cause an immediate crash. 
Something else is wrong.  Please see 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-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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