Re: TIP5P simulation

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jan 07 2012 - 10:18:47 CST

On Fri, Jan 6, 2012 at 11:42 PM, Boyang Wang <pkuwangboyang_at_gmail.com> wrote:
> Hi Sairam,
>
> I was worried if there is a gap between TIP4P and TIP5P models, but now I
> have not seen such a gap.

what "gap" are you talking about?

>
> Probably TIP5P has already been coded into NAMD somewhere, but I think new

where do you conclude this from?

> 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.

what the hell is this supposed to mean?
and what tools exactly are you talking about?

please enlighten me.

thanks,
    axel.

> 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.
>

-- 
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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