On Tue, 2014-05-06 at 12:58 +0530, MOHD HOMAIDUR RAHMAN wrote:
> Dear Amber Users
>
> I am trying to calculate interaction energy between urea-urea, urea-water,
> water-water, water-tmao and urea-tmao molecules with in simulation box. I
> have processed the MD trajectory by using the CPPTRAJ pairwise command as
> suggested by Jason Swails.
Note that cpptraj's "pairwise" function does not use periodic boundary
conditions, leading to potentially serious errors (especially if you do
not image first).
> I am getting total IE as given below
>
> IE(uu) = 50.88, IE(ut) = -6.136, IE (uw) = -15.64, IE(tt) = 19.69, IE (tw)
> = -10.19, IE (ww) = -24.09 , Total IE = 14.51
Have a look at your mdout file. Does this "total" interaction energy
make sense based on the values of the electrostatic or van der Waals
energies that are printed there?
Your expected values may also be getting skewed by intramolecular
electrostatic interactions (remember, only 1-2, 1-3, and 1-4 pairs of
atoms are excluded, but many of your molecules have 1-5 or more
interactions that may contribute positive energies to what cpptraj is
computing).
> The total IE of system should be negative, but I am getting positive "This
> is possible"? The simulation box contain 7.43M urea and 3.71M TMAO. I also
> calculated IE of pure Urea (for cross checking) and that case I am also getting
> positive value ( Is this parameter fault ? ).
>
> Could anyone suggest me, why I am getting this positive value of Total
> Interaction Energy?
I think it's time to break out some pen and paper and start doing some
basic estimates by hand. Try setting up some model systems that you can
calculate by hand and make sure you understand exactly where the
energies that cpptraj computes is coming from. Hopefully that will help
you develop a strategy to compute what you actually want.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 06 2014 - 07:30:06 PDT
