From: Shanshan Wu (swu64_at_uic.edu)
Date: Tue Feb 03 2015 - 18:36:34 CST
Hello all,
Is it possible to use TIP5P run simulation with namd? When I tried to use
TIP5P, it always have some error.
*Warning: FOUND 4658 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO 0.001*
*ERROR*
*ERROR*
*ERROR*
*ERROR*
*ERROR*
..
It seems namd cannot support TIP5P. How can I solve such problems?
There are some special code for TIP4P in namd. Is there anywhere I can get
some code for TIP5P?
[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;
Thanks
Best wishes
Shanshan Wu
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