Mr Justin: I have tried to do energy minimization in this situation which only existing small molecule in water, I found the structure of organic molecule didn’t become distortions. I think the distortions of organic molecules are due to these stronger interactions between small molecules and enzyme, because there is a enzyme molecule in the previous simulation. Do you think this consideration is correct? In the case, do you think this phenomenon is normal? What’s more, I checked out the top file of small molecules and don’t find error and include the information of improper dihedrals.
Thank you very much! Yours, Yujie liu -- 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.
