Re: TIP5P simulation

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 05 2012 - 21:59:12 CST

On Thu, Jan 5, 2012 at 10:41 PM, Mallajosyula, Sairam
<smallajo_at_rx.umaryland.edu> wrote:
> Hi all
>
> Is it possible to simulate TIP5P water using NAMD. I have successfully run this using CHARMM, but due to the system
> size i want to use NAMD. Here are my observations.
>
> 1) NAMD does not recognize the lone pairs in TIP5P water model. This is evident from the following message
>  Warning: FOUND 16764 ATOMS WITH ZERO OR NEGATIVE MASSES!  CHANGED TO 0.001
>
> As a test i used the TIP4 water model and found that it recognized the lone pair.
> Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE USED
>
> *** So is there a key word which enables lone pair recognition.

that is not how this works in NAMD.
there is special code that has the tip4p style geometries hardcoded.

you would need to write something equivalent for tip5p,

from the sources:

[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;

and:

[akohlmey_at_fermi namd2/src]$ grep -i tip5p *
[akohlmey_at_fermi namd2/src]$

axel.
>
> 2) NAMD gives me the following error
> ERROR: Atom 484 velocity is 10430.7 -5415.58 -3101.58 (limit is 12000)
> It is obvious that this is due to the mass less lone pairs.
>
> On searching the namd list i did not find many insights into this. There have been suggestions on imposing
> large force constants. But i do not know is this is the best way to go about it.
>
> I would appreciate some insights into this issue.
>
> Thanks
>
> Sairam
>
> Dr. Sairam S. Mallajosyula
> Post-Doctoral Scholar
> Computer Aided Drug Design Center
> University of Maryland
> Baltimore
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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