VMD-L Mailing List

From: Aleksei (erdelgado_at_udec.cl)
Date: Fri May 22 2020 - 11:50:36 CDT

Is not against protocol, you are supposed to minimize the secondary
interactions.

You can edit the input file using any molecular editor, the water
molecule's coordinates are defined using a Z-matrix, so it suffices to
modify the dihedral of the first atom (either an hydrogen or a dummy
atom) to move the whole water molecule.

El 22/5/20 a las 2:24, Daniel Fellner escribió:
> While running the Gaussian input files, one of the calculations ran into a
> segmentation violation error. Upon visually inspecting the initial
> coordinates of the water, it appears that it's very close to one of the
> other rings in my system. Is there some way to manually place this on the
> other side (the opposite site of the ring is unobstructed)? Or would that
> not be according to protocol? If not, how should I proceed?
>
>
> *Daniel Fellner BSc(Hons)*
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326
>