[gmx-users] LINCS warming, but continued EM

[Justin Lemkul]

On 10/28/16 12:35 PM, Mijiddorj Batsaikhan wrote:
> Dear gmx users,
>
> I manually added few atoms in my initial structure that was generated by
> Charmm-gui. Then I run EM, but early of minimization LINCS warns appeared,
> minimization continued and finished.
>
> (1) What can I do in this situation?
>
> (2) Is EM reasonable enough?
>
>

You probably introduced some bad clashes when you added atoms, so the initial 
steps were pretty nasty.  If minimization continued and produced a reasonable 
Fmax with a sensible geometry, then it's fine.

-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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