Re: [AMBER] Ewald force using debugf

From: Zhenyu Meng <fdmm1989.gmail.com>
Date: Wed, 4 May 2016 11:28:42 +0800

Dear David Case,
Sorry for my vague expression.
Actually my purpose is to fix some bugs of my code to calculate Ewald
summation.
I have already confirm my energy with GROMACS output, but GROMACS cannot
give each component of force, so I try to use Amber to give such result.
I try to make sure the input script is exactly consistent with the standard
Ewald summation, so that I can figure out where the error of my code is.
Attached please find 3 output files, ELECTRO3.dat is from my code and the
other 2 is from Amber. I also attach the corresponding input files, the
only difference is in debug2.in eedmeth=1.
To make the problem simpler, my system only contains 2 water molecules.
The force unit in my code is (mu*A/fs^2), so to convert the value in
forcedump.dat to mine, just multiply it by 4.184E-4.
My code does not consider adjust sum, while for both direct sum and
reciprocal sum, the value, as well as the sign, deviated a lot.


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2016-05-03 22:48 GMT+08:00 David A Case <david.case.rutgers.edu>:

> On Tue, May 03, 2016, Zhenyu Meng wrote:
>
> > I tried to let ew_type=1, while still I got different result.
>
> You will have to try harder to explain what you mean. I'm not able to
> understand (at all!) what you mean by a "different result".
>
> > BTW, is the adjust sum electrostatic in forcedump.dat an adjustment for
> > cutoff correction?
>
> No. It represents the fact that certain electrostatic interactions
> involving
> 1-2, 1-3, and 1-4 atom pairs are treated in a special way in molecular
> mechanics force fields. The Ewald sum code first ignores this fact, then
> "adjusts" the final answer to take it into account.
>
> ...dac
>
>
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>



-- 
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University







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Received on Tue May 03 2016 - 20:30:04 PDT
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