From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Fri Oct 02 2015 - 01:16:41 CDT
Shanshan,
Did you get an answer for this question? If so please share it with me. I
am also struggling with the same question.
Regards,
Monika
On Wed, Feb 4, 2015 at 6:06 AM, Shanshan Wu <swu64_at_uic.edu> wrote:
> 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
>
>
>
-- W.A.Monika Madhavi Lecturer (Probation), Department of Physics, University of Colombo.
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