Re: What is a good (small) test system for NAMD

From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Tue Jul 10 2012 - 15:43:20 CDT

Hi Aron,

Thanks, I will see what I can do with this information .

Roy

On Tue, Jul 10, 2012 at 4:19 PM, Aron Broom <broomsday_at_gmail.com> wrote:

> I agree with your definition of non-bonded really meaning non-covalently
> bonded.
>
> For the two Na+, I'm not sure, it may be the repulsion as you say, it
> could be the periodic box was too small, maybe you need to gradually heat.
> If you use Argon, while it's true that they will not have a charge, they
> will still have an interaction energy as a result of the van der Walls
> forces, so there will be an energetic minimum with them being "attached"
> much as your protein dimer would be (presumably your dimer interface is
> largely hydrophobic, and therefore has limited partial charge).
>
> I think the two TIP3P water system would be a good bet also, since the
> dependence on geometry might be analogous to your dimer. You can readily
> use the built in MetaDynamics code in NAMD to get an accurate potential of
> mean force (PMF) for pulling apart the water dimer along for instance a
> center of mass distance reaction coordinate. It might take at most a day
> on a single CPU core. You could of course do the same thing with the argon
> dimer or Na+ and Cl-, in order to see what the "real" PMF (given
> limitations of the forcefield) is for your system.
>
> ~Aron
>
>
> On Tue, Jul 10, 2012 at 4:07 PM, Roy Fernando <roy.nandos_at_gmail.com>wrote:
>
>> Hi Aron,
>>
>> Thank you very much for your input.
>>
>> I think what you are saying make sense. I did not think about the
>> connection part.
>>
>> When you say non bonded I am little bit confused about the meaning. My
>> background is physics.I think what you are saying is non covalently bonded.
>> I want to apply tcl forces to a system of a protein dimer. This dimer is
>> not connected through covalent bonds. I want to simplify the dimer so that
>> a single unit contains only one atom. So this is a non bonded system.
>>
>> I will try to generate the psf removing the connectivity information.
>>
>> The other question I am having is why it is not possible to equilibrate
>> the two Na+ atom system. Do you think it is because of the magnitude of the
>> electrostatic repulsion between the two toms? What do you think, i should
>> do to overcome this problem? If I use Argon atoms instead of Na+ will the
>> problem solved. But I wonder if I would be able to see any response to
>> applied forces as they behave as non interacting rigid particles.
>>
>> Regards,
>>
>> Roy.
>>
>>
>> On Tue, Jul 10, 2012 at 3:46 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>>
>>> why are you trying to bond them?? Those atoms are designed to be ions
>>> in solution. It sounds from your earlier email like you want two
>>> non-bonded atoms, so I'd remove the connect and put a TER between the two.
>>>
>>> If you really do want a two atom, one molecule system, that is a bit
>>> different.
>>>
>>> ~Aron
>>>
>>>
>>> On Tue, Jul 10, 2012 at 3:34 PM, Roy Fernando <roy.nandos_at_gmail.com>wrote:
>>>
>>>> Hi Giacomo,
>>>>
>>>> I could not generate a psf file to NA-Cl. I have the pdb file for
>>>> Na-Cl. It looks simple.
>>>>
>>>> HEADER
>>>> COMPND Sodium Chloride
>>>> AUTHOR Peter Carr
>>>> ATOM 1 Na SOD 1 0.000 0.000 -1.200 1.00 0.00
>>>> ATOM 2 Cl CLA 1 0.000 0.000 1.200 1.00 0.00
>>>> CONECT 1 2
>>>> CONECT 2 1
>>>> END
>>>> But when I tried to generate the psf file for this one, it always
>>>> complained about not recognizing the coordinates and eventually produced a
>>>> file without Cl- atom in it.
>>>>
>>>> Something like the following.
>>>>
>>>> REMARK original generated coordinate pdb file
>>>> ATOM 1 SOD SOD X 1 0.000 0.000 0.000 -1.00 0.00
>>>> U NA
>>>> END
>>>> Then I tried to do the same thing with shifted NA-Cl molecule like
>>>> following, but still the result is same
>>>>
>>>> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
>>>> ATOM 1 Na SOD A x 1.000 1.000 -0.200 1.00
>>>> 0.00
>>>> ATOM 2 Cl CLA A x 1.000 1.000 2.200 1.00
>>>> 0.00
>>>> END
>>>> Have you done this before?
>>>>
>>>> Regards,
>>>>
>>>> Roy
>>>>
>>>> On Tue, Jul 10, 2012 at 3:17 PM, Giacomo Fiorin <
>>>> giacomo.fiorin_at_gmail.com> wrote:
>>>>
>>>>> If you want to stick to two atoms, why not Na+ Cl-? :-)
>>>>>
>>>>>
>>>>> On Tue, Jul 10, 2012 at 3:13 PM, Roy Fernando <roy.nandos_at_gmail.com>wrote:
>>>>>
>>>>>> Dear All,
>>>>>>
>>>>>> I am looking for a small test system to test my TCL forces
>>>>>> simulation. Ideal case is a two atom system. Can anyone of you suggest what
>>>>>> is a good system for this purpose.
>>>>>>
>>>>>> I will be grateful if someone would like to share a pdb and psf
>>>>>> files. I actually made a pdb and psf files by putting two Na ions in to a
>>>>>> water box. But I could not equilibrate this system. System becomes
>>>>>> unstable, when the velocities are applied after the minimizing at 0k
>>>>>> temperature. A two atom system is subject to a Lenard Jones type potential
>>>>>> and therefore the energy curve is known. That is why I am interested on two
>>>>>> atom systems. Also it is the least complex system for testing an algorythm.
>>>>>>
>>>>>> What test systems you guys are using?
>>>>>> I appreciate your suggestions.
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Roy
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>

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