Hello,
The form of umbrella restraints and SMD restraints are the same, the only
difference is that the equilibrium location of the SMD restraints changes
with time and for umbrella sampling, it doesn't. You should be able to use
LCOD for umbrella sampling.
However, the LCOD implementation in sander that I use is already built into
the NMR restraints in amber10 (see the appropriate section of the Amber10
manual), so I'm not quite sure how to use the NCSU codes to do it.
Good luck!
Jason
On Fri, Aug 6, 2010 at 3:46 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> I am interested to study a reaction coordinate as follows:
>
>
>
> X + C-Y ==> X-C-Y ==> X-C + Y
>
>
>
> It seems to me that I should define the reaction coordinate as the
> distances of XtoC and CtoY.
>
>
>
> The LCOD patch used in tutorial A10 seems to serve this purpose for Steered
> MD calculation.
>
>
>
> However, if I am doing PMF with umbrella sampling, can I should use the
> LCOD commands?
>
>
>
> Best regards,
>
>
>
> Cat
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Aug 06 2010 - 06:00:12 PDT
