[gmx-users] Solvating in a solvent other than water

Justin Lemkul jalemkul at vt.edu
Mon Sep 21 14:19:26 CEST 2015

On 9/21/15 12:13 AM, Pallavi Banerjee wrote:
> Yes, I should have put up the images.
> I have uploaded two images, one of the expanded box before energy
> minimization and the other after, which shows the formation of blocks. I
> performed an NVT equilibration with this bad, 'block'ed box, and too many
> LINCS warning show up.
> 1. Before minimization:
> https://drive.google.com/file/d/0B0oti29Tm3S2VFhheVJ5SFBKQ1E/view?usp=sharing
> 2. After minimization:
> https://drive.google.com/file/d/0B0oti29Tm3S2VGd5SnpZTDVhYUE/view?usp=sharing

Looks like you probably didn't make the molecules whole before replicating the 
box; the molecules at the edges look distorted, but it's a bit hard to tell.



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


More information about the gromacs.org_gmx-users mailing list