[gmx-users] Energy minimization problem after editconf step

Justin Lemkul jalemkul at vt.edu
Tue Sep 2 14:52:55 CEST 2014

On 9/2/14, 7:12 AM, neha bharti wrote:
> Hello All
> I am trying to perform MD for protein ligand complex in popc lipid with
> Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane
> protein simulation.
> I have successfully perform till InflateGRO followed by energy minimization
> step.
> perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat
>   grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr
> mdrun -v -deffnm em
> till 24 iteration then I reached area per lipid 0.70 nm^2
> when I visualize the molecule then the box size small in Z axis so in
> editconf step I increase the box size and then add solvent and ion . when I
> increase the box size with editconf then there is atomic clashes occur.and
> giving following error:
> Steepest Descents converged to machine precision in 18 steps,
>   but did not reach the requested Fmax < 1000.
>   Potential Energy  =  6.1499341e+20
>   Maximum force     =            inf on atom 3300
> Norm of force     =  5.4206209e+1
>   When I skip this step (editconf) then the minimization is normal.
> But I need to increase the box size.
> How to increase the box size?

You need to provide the exact commands that you used when manipulating the box, 
otherwise it's pure guesswork.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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