From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Tue Jul 10 2012 - 14:34:40 CDT
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
>>
>
>
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