[gmx-users] Energy minimization problem after editconf step

neha bharti nehabharty123 at gmail.com
Tue Sep 2 13:12:53 CEST 2014

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

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?

Please help

With Regards
Neha bharty

More information about the gromacs.org_gmx-users mailing list