No. Bonded interactions (such as distance restraints) can only be defined between atoms present in the same [moleculetype]. OTOH a [moleculetype] doesn't care whether any bonded interactions exist between its atoms or not, so as long as you obey the constraint that the atom ordering implied by your [molecules] ordering and ordering of [atoms] within [moleculetypes] must match that of the coordinate file given to grompp, you're fine. Atom numbering in the coordinate file to grompp is not important (but you get told if there's mismatches, IIRC).
Mark On Tue, Dec 11, 2012 at 7:23 AM, Yun Shi <yunsh...@gmail.com> wrote: > Hi all, > > I want to restrain the OW of a bound water molecule for the MD of a > protein in water. But the index of this OW is apparently out of range > and I know someone would suggest merging this water with my protein > (e.g. put them in the same .itp file) so as to make them "one > molecule" and thus the index would not be out of bounds. > > But I wonder if there is any other way to circumvent this issue? > > Thanks, > Yun > -- > 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 > -- 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
