Dear Gromacs Users, I noticed that quite often after adding the solvent (water) to the protein, the water molecules fill in gaps inside the protein which are not occupied. I am afraid that since their position may not be optimal (they actually should not be there), it will lead to artifacts as the MD simulation progresses. What is your opinion on removing these water molecules on some occasions?
Best wishes, Dawid Grabarek -- 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.
