[gmx-users] How to remove charge of 5e-2 ??

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 5 15:32:14 CEST 2011

Hyunsik wrote:
> Dear experts,
> Hi, 
> When prepare a system, the system had +5.5. So I add 5 CL- ion to neutralize.
> But as you know, the Cl charge is -1 and there still is 5e-2. how can i remove that.
> i want to make totally neutral system.

Fractional charges like these indicate that your topology is broken.  Check its 
contents (especially the qtot running total if the .top was created by pdb2gmx).


> Thank you.
> Hyun-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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