Dear Justin Thanks for your time and consideration.
> As I suggested before, visualize the output file and figure out what is > around atom 618 to cause such forces. I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc molecule (this dopc molecule is intact and is not broken). There are other dopc and cholesterol molecules around atom 618. How I understand what around this atom cause such forces. Excuse me. Please give me more explanation about your suggestion. May be, I did not understand your mean truly. Should I remove this dopc molecule and then run minimization again? > PRODRG generates notoriously bad parameters, particularly the charges. I know this issue, charges and charges groups obtained from prodrg (in itp file) were compared with charges and charges groups in similar structures being in rtp file of gromos (because my drug is very similar to cytosine). Then I corrected them. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
