[gmx-users] Energy minimization problem after editconf step
nehabharty123 at gmail.com
Tue Sep 2 13:12:53 CEST 2014
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
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?
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