From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Oct 12 2015 - 05:10:35 CDT
In Molecule.C and Homepatch.C files the lone pair position of tip4p water
is defined as follows.
r_ohc = sqrt(r_oh * r_oh - 0.25 * r_hh * r_hh)
pos = pos + (0.5 * (pos + pos) - pos) * (r_om / r_ohc);
0,1,2 are O,H1,H2 respectively. But the position of lone pair in tip5p
cannot be defined with respect to positions of 0,1,2 alone. I don't have
knowledge on C programming. Could someone please let me know how to define
the position of lone pair incorporating the angle between the H-O-H
bisector and O-LP bond?
On Mon, Oct 12, 2015 at 2:14 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> Yes Peter,
> 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.
> Best regards,
> 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.
-- W.A.Monika Madhavi Lecturer (Probation), Department of Physics, University of Colombo.
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