[gmx-users] LINCS warming, but continued EM

Mijiddorj Batsaikhan b.mijiddorj at gmail.com
Sat Oct 29 13:44:57 CEST 2016


Dear Justin,

Thank you very much for your all helps.

(1) How can I easily reduce these clashes? Is there any good software?

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


Best regards,

Mijiddorj



>
>
> 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
>
> --
> ==================================================
>
> 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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