From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Oct 12 2015 - 03:44:50 CDT
Actually I found the place and how it is defined. It is defined in
Molecule.C file. However tip5p geometry is significantly different from
tip4p. Tip4p lone pair is along the bisector of the H-O-H angle but, tip5p
lone pairs are in a perpendicular plane to the HOH plane. I am trying to
define the position of tip5p lone pair with respect to positions of H and
O atoms. If someone can guide me, that would be great.
On Sun, Oct 11, 2015 at 8:03 AM, Peter Freddolino <petefred_at_umich.edu>
> Did you try grepping the source code for r_ohc?
> > On Oct 9, 2015, at 6:29 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
> > Dear all,
> > I am trying to simulate TIP5P water with namd. I am trying to hardcode
> TIP5P as TIP4P is done in namd. However in Homepatch.C file, the parameter
> r_ohc is defined as the altitude of hydrogen center of mass from oxygen.
> Can someone please tell me on which file this calculation is done?
> > Best regards,
> > Monika
> > --
> > W.A.Monika Madhavi
> > Lecturer (Probation),
> > Department of Physics,
> > University of Colombo.
-- W.A.Monika Madhavi Lecturer (Probation), Department of Physics, University of Colombo.
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