[gmx-users] Water molecule starting at atom 39087 can not be settled

[Justin Lemkul]

On 3/21/17 7:08 PM, liming_52 wrote:
> The position of the ligand was obtained using autodock vina. The gro file and ITP file were obtained from the PRODRG server (http://davapc1.bioch.dundee.ac.uk/prodrg). Anyway, I added the ions with 0.154 M NaCl. Did these effect my md?
>

PRODRG topologies are of insufficient quality for MD simulations.  If you want 
to use GROMOS, try ATB instead.  Or investigate other parametrization tools for 
other force fields.  If you have a new topology and it's still not stable, 
follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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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