[gmx-users] problem in energy minimization of protein in lipid membrane

[Justin Lemkul]

On 11/19/14 12:32 PM, Padmani Sandhu wrote:
> Helllo all,
>
> I am facing problem with energy minimization of system after reaching
> desired area per lipid. System is not converging to Fmax < 1000 during
> final energy minimization. I have turned off all strong position restraints
> for protein.
>

What are the actual values of Fmax and Epot from mdrun?  Note that it also 
prints out the atom bearing Fmax, so that is your first indication of where 
problems may be.  Visualize the output and see what you can learn.

-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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