[gmx-users] LINCS warming, but continued EM

[Justin Lemkul]

On 10/29/16 7:44 AM, Mijiddorj Batsaikhan wrote:
> Dear Justin,
>
> Thank you very much for your all helps.
>
> (1) How can I easily reduce these clashes? Is there any good software?
>

You're using it.  The point of energy minimization is to relax the structure. 
It just so happens that you have some nasty ones.

> (2) from geometrical view, EM.gro structure looks fine. However, there are
> many individual protons separated from Lipid molecules. Is this usual?
>

Depends on the distance.  Visualization software typically renders bonds based 
on assumptions about bond lengths.  If the X-H bonds are actually longer than 
they should be, then your topology is probably wrong or the initial bad geometry 
caused distortion of the structure that couldn't be resolved.  Typically, the 
result will be bad forces that do not converge below a sane tolerance, though.

-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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