AMBER Archive (2008)

Subject: Re: AMBER: How do you evaluate forces on a fixed atom?

From: Bill K (bill_at_mercury.chem.pitt.edu)
Date: Tue Dec 02 2008 - 19:54:35 CST

> On Mon, Dec 01, 2008, Bill K wrote:
>
>> Has anyone tried to extract the systematic forces on a fixed
>> atom, or may know how to do it? I'm using amber7 and, if you have an
atom fixed in the system, the forces on it are canceled before they can be
evaluated. That is to say, output prints values of 0.0 0.0 0.0 for the
force on a fixed atom, even though it experienced forces from the
surrounding atoms. Looking at the code, this occurs because ibelly sets
these values to zero. It looks like this task is not possible without
changing the source code.

>
> I agree: you would have modify the code to print out the forces before
the ibelly step sets them to zero. I'm pretty sure this
> has not changed in more recent releasees.
>
> ...dac
>

Dr. Case,
     Thank you very much for your reply. Is there any short
script/insertion point to print out the forces of a select
atom that you may recommend that won't break the code? I'd rather
ask the expert before posting a solution on here that may cause new
problems for people - it seems like it may be a potentially useful
tool for users. If not, I can keep testing things until I'm
confident in an answer. Please don't waste your time on it.
     I appreciate your time and consideration.
         -Bill

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