# Re: [AMBER] Pairwise vs Sander with imin=5

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 19 Nov 2014 22:14:27 -0700

Hi,

I think that 1-4 electrostatics/van der Waals terms are included for
idecomp energy decomposition 2 and 4; the 'pairwise' cpptraj command
does not calculate these, so that may be where your differences are
coming from (others who are more idecomp-savvy may want to correct me
here). The total EEL/vdW energies I get from cpptraj match sander
exactly.

-Dan

PS - By the way, what version of cpptraj are you using?

On Wed, Nov 19, 2014 at 7:01 PM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear amber developers and uses,
>
> I'm now using "pairwise" in cpptraj to
> Calculate inter-residue energy.
>
> Assuming residues A and B,
> I calculated energy three times, i.e., for A, B and A+B.
> Finally, I got inter-residue energy as Ene(A+B) - {Ene(A) + Ene(B)}.
>
> Now, I compaired the value with that obtained from sander with imin=5, and
> idecomp = 4.
> It is "almost" a half of the "pairwise" value.
> I am assuming that "sander value" is divided by two
> To assign inter-residue energy for each residue.
>
> Is this observation right?
>
> Even so, I found the difference between sander and pairwise by ca 1 kcal/mol,
> (for pairwise and sander, -96.6274 and -94.492 (2 x -47.246) [kcal/mol],
> respectively)
> Although I used the same value for non-bonded cutoff of value, 99 [A] for each
> computation.
>
> Considering that each calculation is executed under the vacuum.
> This inconsistensy seems strange.
> Is there any additional difference between sander and pairwise?
>
> Thank you for your support.
>
> Best regards,
>
> Ikuo KURISAKI
>
> PS
>
> I believe "idecomp =3 or 4" does not make difference
> When inter-residue energy is calculated.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

```--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
```
Received on Wed Nov 19 2014 - 21:30:03 PST
Custom Search