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.
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
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?
Thank you in advance.
Regards
Rahman
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Received on Tue May 06 2014 - 01:00:03 PDT
