simulating tip5p water

From: Monika Madhavi (
Date: Thu Oct 01 2015 - 23:36:51 CDT

Dear all,

I need to simulate a tip5p water box with NAMD. I have the pdb and psf
created. According to my experience of simulating with water models like
tip4p, the configuration parameter waterModel should be set to tip4 in
addition to topology and parameters to preserve the shape of the molecule
during simulation. But tip5 model is not supported by NAMD. It is suggested
that, tip5p style should be hard corded as tip4p using the following

[akohlmey_at_fermi namd2/src]$ grep -i tip4p *
HomePatch.C:// be using tip4p
HomePatch.C: // initialize the distances needed for the tip4p water model
HomePatch.C: * This is done using the same algorithm as charmm uses
for TIP4P lonepairs.
HomePatch.C: /* Reposition the om particle of a tip4p water
HomePatch.C: * Ordering of TIP4P atoms: O, H1, H2, LP.
HomePatch.C:void HomePatch::redistrib_tip4p_forces(const int ftag,
Tensor* virial) {
HomePatch.h: // PLF -- for TIP4P
HomePatch.h: //void redistrib_tip4p_force(Vector&, Vector&, Vector&,
Vector&, int, Tensor*);
HomePatch.h: void redistrib_tip4p_forces(const int, Tensor*);
HomePatch.h: // use for both TIP4P and SWM4 water
Molecule.C: // If we have TIP4P water, check for lone pairs
Molecule.h: // data for TIP4P
Sequencer.C: patch->redistrib_tip4p_forces(Results::normal, &virial);
Sequencer.C: patch->redistrib_tip4p_forces(Results::nbond, &virial);
Sequencer.C: patch->redistrib_tip4p_forces(Results::slow, &virial);
SimParameters.C: iout << iINFO << "Using TIP4P water model.\n" << endi;

Is there anyone who has done this and would like to share how you added the
functions for tip5p? Can we use swm4 watermodel as a guide to hard cord for

Thanks in advance.

Best regards,

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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