Re: [AMBER] Apply Lennar-Jones potential between small molecules

From: David A Case <>
Date: Tue, 16 Mar 2021 08:55:43 -0400

On Tue, Mar 16, 2021, Carlos Simmerling wrote:

>yes negative rk gives an inverted parabola, so it is repulsive if it is
>outside the flat region.

I'm a little confused here, and would recommend careful testing if you are
setting rk2 to a negative number. I've not done that but it *sounds*
dangerous. Probably a good idea to numerically plot the function vs.
distance, and make sure you are getting the behavior you want.

>> should rk2 be negative when applying repulsive for between two groups
>> closer than r2? When I set it to 50, the two groups are close but the
>> restrain in output file is 0.

If you do a one-step calculation with LISTIN=POUT, you will see additional
details of exactly how the restraints are being implemented. Try with a
starting structure where you expect a restraint but don't get one. This may
help in tracking down the problem.


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Received on Tue Mar 16 2021 - 06:00:03 PDT
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