[gmx-users] gold-S simulation

[Justin Lemkul]

On 12/19/12 6:02 AM, fatemeh ramezani wrote:
> Dear Justin
>
> I want exactly this, that the distance between Au-S be stable around equilibrium value, For this purpose,Should I put the harmonic parameters related to the  gold and sulfur  in ffbonded file? Or I should consider AU-S connection as VonderWaals and put its epsilon and sidma in ffnonbonded file?
>

Please be mindful to only parse the relevant portion of the digest and to use a 
real subject line.

Yes, if you want there to be a covalent bond, you need to introduce one.  Hoping 
that van der Waals parameters will hold the elements of the system in place does 
not sound like a robust approach to me.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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