VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon May 16 2016 - 10:26:03 CDT

Mohan,

Sorry for the delayed reply.

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

This will in all likelihood resulting in strong steric clashes. The minimizer may take care of these; however, you may end up with ring piercing events that cannot be minimized properly.

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

I looked at my scripts that I used to setup these calculations for the initial ffTK paper. We set the grid spacing using the longest distance across the molecule. For non-spherical shapes this results in a grid that starts off too large, but it prevents the clashes described above.

Regards,
Christopher Mayne

> On May 12, 2016, at 12:42 PM, Mohan maruthi sena <maruthi.sena_at_gmail.com> wrote:
>
> 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