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

From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jul 10 2012 - 15:19:01 CDT

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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