There will be a harmonic restraint applied to a reaction coordinate. The
force constant will be 200 (kcal/mol)/A^2 and the center of the
restraint will move from -6.09 to -2.0 in nstlim steps (nstlim is in the
main namelist)
The reaction coordinate is defined as the sums and differences between
FOUR distances.
RC = -d1 + d2 - d3 -d4
d1 = distance between atoms 4536 and 3483
d2 = distance between atoms 3483 and 3482
d3 = distance between atoms 3482 and 3487
d4 = distance between atoms 3488 and 19505
Is this clear ?
adrian
> Hello Amber Users,
>
> Can anybody explain me the meaning of the following input file used for a
> SMD run?
>
> #Reaction coordinate
> #Dist H3OH-Os, Os-S, S-N y HN-Owat
> &rst iat=4536,3483,3483,3482,3482,3487,3488,19505, rstwt=-1,1,-1,-1,
> r2=-6.09, rk2=200, r2a=-2.0, /
>
> H3OH-Os, Os-S, HN-Owat : involves bond break and atom transfer
> S-N : involves bond formation
>
>
>
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Jul 25 2016 - 00:30:03 PDT
