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? Please help With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.