On Wed, Aug 11, 2010 at 5:55 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear All,
>
>
>
> I would like to calculate a PMF for a reaction coordinates which involve
> forming bond between A-B, at the same time cleaving a bond between B-C.
>
>
>
> I learnt from Bud that I may use "generalized distance coordinate
> restraint" to set the restraint and define the reaction coordinates. I
> lookup the manual. I found the restaint is defined as
>
>
>
> U = k(w1|r1-r2|+w2|r3-r4|+w3|r5-r6|+w4|r7-r8|-r0)2
>
>
>
>
>
> Is it same as the restrainst defined for LCOD?
>
>
>
> I also want to reconfirm with you that if I should define the restraint
> files as follows, if I want to study the PMF when LCOD change from 1A to
> 10A?
>
>
> # reaction coordinates
> &rst iat(6)=A,B,B,C, r1=0., r2=1., r3=1., r4=10., rk2 = 30., rk3 = 30., /
>
This should be iat, not iat(6). You also need numbers here, not letters,
but I assume you knew that. If you want a generalized distance restraint,
you also need to define the restraint weights (rstwt). Then that will be a
generalized distance restraint for the 2 distances. The restraint weights
are the w1, w2, ..., etc. in the formula you posted above.
Good luck!
Jason
>
> Best regards,
>
> Catherine
>
>
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Aug 11 2010 - 06:00:06 PDT
