Re: TIP5P simulation

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Fri Jan 06 2012 - 22:42:07 CST

Hi Sairam,

I was worried if there is a gap between TIP4P and TIP5P models, but now I
have not seen such a gap.

Probably TIP5P has already been coded into NAMD somewhere, but I think new
nice application is needed if you have tools available around. It should be
around, if you have access to the tools. The model itself does not rely on
the software we are coding, and very likely you will get very unexpected
results, if you try well.

Best,
Boyang

On Fri, Jan 6, 2012 at 11:58 PM, Mallajosyula, Sairam <
smallajo_at_rx.umaryland.edu> wrote:

> Hi Axel
>
> Thanks for the information. This clears up a few doubts with regards to the
> redistribution of forces.
>
> I would definitely try to set this up. But if someone has already hard
> coded TIP5
> into NAMD then could they share the same with me.
>
> Thanks
>
> Sairam
>
> ________________________________________
> From: Axel Kohlmeyer [akohlmey_at_gmail.com]
> Sent: Thursday, January 05, 2012 10:59 PM
> To: Mallajosyula, Sairam
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: TIP5P simulation
>
> 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.
>
>

-- 
Boyang Wang, Ph.D.

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