[gmx-users] genion error sol not continuous

[Justin Lemkul]

On 5/14/15 1:25 AM, James Lord wrote:
> Hi all,
> I am trying to neutralize this system (1HFX.gro) and genion is complaining
> about solvent not being continuous,then I made the 1HFX_modified.gro in
> which
> I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end of
> the file. I am expecting gromacs to do the reordering for SOL. Am I missing
> anything?

The topology needs to be modified in a similar manner.  IIRC it is topological 
continuity that genion checks.

-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

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