From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Tue Jul 10 2012 - 15:07:05 CDT
Thank you very much for your input.
I think what you are saying make sense. I did not think about the
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.
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
> 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.
>> 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
>> 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
>> 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
>> ATOM 2 Cl CLA A x 1.000 1.000 2.200 1.00
>> Have you done this before?
>> 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.
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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