Re: [AMBER] Force constant

From: Nicholas Musolino <musolino.MIT.EDU>
Date: Sun, 18 Apr 2010 12:08:14 -0400

On Apr 18, 2010, at 11:54 AM, William Flak wrote:
> Dear users
> I am trying to optimize two molecules interacting together using AMBER. The interaction takes place on a lone pair (treated as EP in AMBER).Minimization should be in gas phase, I used the following input file, could you check it? &cntrl imin = 1, maxcyc = 1250, ncyc = 1000, ntb = 0, ntr = 0, cut = 999 /
> In fact, I got a weird data, if I changed the force constant for the bond length between EP and X from 500 to 600, the interaction between lone pair (on one fragment) and the other fragment completely changed. Why?Thanks

Dear William,
I don't think I'm experienced enough with AMBER to evaluate the details of your input file.

To evaluate the underlying physical/numerical issue, however, I think we'll need more information. What do you mean when you say the "interaction completely changed"? Do you mean the interaction energy, or the geometry? I agree with your implication that a drastic change would be unexpected.

Also important would be to understand which force field you're using, and how you're obtaining parameters for these molecules. What kind of molecules are they?

Zooming out a bit, my instinct is to be cautious with lone pairs, as others have suggested on this list before (see

If you write back with more info, we might be able to make more suggestions. Best of luck,
Nicholas Musolino

PS. Don't know if it's a mail client issue on your end or my end, but your e-mail came through with no line breaks, at least in my inbox.
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT | 617-253-6675 | Room E19-528

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Received on Sun Apr 18 2010 - 09:30:02 PDT
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