On Wed, 2014-04-16 at 17:46 +0530, MOHD HOMAIDUR RAHMAN wrote:
> Dear Jason and Amber Users
>
> In my simulation box I have Urea and Water and now I want to calculate the
> average Interaction energy between Urea_Urea, Urea_Water and Water_Water.
>
> For this I process the trajectory to get Average Interaction Energy as
> Jason suggested me to used the pairwise command from cpptraj.
>
> By this method I am able to reproduce the average interaction energy of
> water_water but fail to reproduce the Average interaction energy between
> urea_urea and urea_water.
>
> I given the input for cpptraj.
> .........................................................................................................
> trajin urea_wat.crd
>
> pairwise U_U :URA out pairwise_uu.dat cuteelec 12.0 cutevdw 12.0
> pairwise S_S :SPC out pairwise_ww.dat cuteelec 12.0 cutevdw 12.0
> pairwise U_S :URA,SPC out pairwise_us.dat cuteelec 12.0 cutevdw 12.0
> ...........................................................................................................
>
> The output file for Urea_Urea
> ..........................................................................................................
> #Frame U_U_EVDW U_U_EELEC
> 1 -155.2368 4250.4339
> 2 -173.2890 4371.9059
> 3 -173.9027 4314.2041
> 4 -175.4758 4346.7265
> 5 -185.3734 4374.9934
>
> ...
> ...
> 2495 -191.3443 4315.2169
> 2496 -167.5771 4325.8357
> 2497 -163.5134 4351.2010
> 2498 -179.8482 4369.4136
> 2499 -169.7458 4278.9632
> 2500 -166.5782 4314.6092
> ...............................................................................................................
>
> After switch off the cutoff value and the output value is giving same.
>
> Here I am unable to understand why Urea_Urea Interaction energy have
> positive value and vander wall have negative value ?
van der Waals always gives a negative value unless the interparticle
separation is less than the combined sigma parameter.
The electrostatic interaction is positive probably because there are
more orientations between 2 urea molecules that are unfavorable than
there are favorable orientations (there are 2 amine groups but only one
carbonyl).
Also keep in mind that a hard cutoff for electrostatic energies is
horrible (it's much better to do some sort of force and/or
energy-shifting, a reaction field, or even better full Ewald
electrostatics). If the charge on a hydrogen is 0.4 electrons, then the
energy between two of these particles separated by 12 angstroms with a
12 angstrom cutoff is 4.42 kcal/mole. At 12.00000001 angstroms the
energy drops to 0, which is a pretty severe discontinuity that can very
rapidly accumulate errors.
Are you sure you don't want some other metric, like maybe a radial
distribution function (pair correlation function) that you could use to
back out a free energy?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 16 2014 - 06:00:04 PDT
