On Wed, Nov 16, 2011, najmul arfin wrote:
>
> i want to change the parameter for H-Bond (10-12 potential ) in TIP3P water
> model , but what i have seen in parm99.dat file that parameter for
> H-Bond is all set to 0.00, rather every thing is calculated using 6-12
> potential . So i have followign question
>
> 1. Will 6-12 potential will always take care of H-Bond , because H-Bond is
> limited between O-H, N-H atoms and is limited for a fix distance ( hydrogen
> bond distance ).
I think there is a language problem here. The TIP3P model per se has no 10-12
terms. The Amber code pretends that these exist, but gives them coefficients
of zero, so that in fact nothing is calculated.
If you want to explore what would happen with different 10-12 terms, you
can change the zero values in parm99.dat to some other values. You would
also have to recompile sander with the -DHAS_10_12 flag set. Making this
change would change the way the OW-HW interactions are computed.
All this has very little to do with chemist thinks of as "hydrogen
bonds" however. None of the individual terms in the Amber force field
corresponds to a "hydrogen bond"; rather H-bonds arise from two features:
1. electrostatic interactions between partial charges
2. the presence of unphysically small van der Waals term for hydrogen, which
allows the donor and acceptor atoms to come closer than the sum of their
van der Waals radii.
> 2. How can i play with the H-Bond in TIP3P water model or how can i play
> with the no. of possible hydrogen bond in a box of TIP3P water
If you are using "H-bond" in a chemical sense here, there is no simple way to
do what you are requesting.
....dac
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Received on Wed Nov 16 2011 - 14:00:02 PST
