Do you have Matlab, Zhenyu? I'll send you my Matlab code in a private
message (also works in octave, I believe) for computing SPME quantities. I
don't think that it does pair exclusions, but if you have just a system of
ions then it should be fine. You might be able to use this to debug your
own code. Another option would be to use mdgx in runmode = 2 (check out
the built in manual by running ${AMBERHOME}/bin/mdgx -FORCE and this will
give you a more complete treatment of your system, including all
topological details, atom by atom. It will also put information into a
file "forcedump.dat" by default (you can change the name), and all
information that would be in sander &debugf output will be encapsulated in
a matlab or octave readable script, in a structure variable whose name you
can set. If you want to make multiple such scripts for comparing different
conformations, you can then put the results in different structure
variables and manipulate the outputs as you wish.
The other Dave C
On Tue, May 3, 2016 at 10:48 AM, David A Case <david.case.rutgers.edu>
wrote:
> 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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Received on Tue May 03 2016 - 12:30:03 PDT
