VMD-L Mailing List

From: Mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Thu May 12 2016 - 12:42:51 CDT

Hi all,
           I have generated parameters for a molecule using fftk. In fftk
article (rapid parametrization of small molecules using fftk) it is
described to calculate density, enthalpy of vaporization and free energy
of solvation for validation of parameters. To calculate enthalpy of
vaporization a 6*6*6 grid of molecules needs to be considered and each
molecule is placed such that the center of mass coincides with grid point .
My question is as follows:

Q1) is it ok if we place 216 molecules randomly in a box of size 6*6*6?

Q2) Could you please elaborate regarding constructing the grid of 6*6*6?
What should be the distance between two grid points? 

-- 
Thanks and Regards,
Mohan Maruthi