VMD-L Mailing List

From: Vivek Sharma (vivek.viv.sharma_at_gmail.com)
Date: Fri May 18 2012 - 06:23:52 CDT

Hello,

There are number of approaches, some I know are:

a) DOWSER - works well on a static structure - interaction energy based
approach.
b) GCMC in CHARMM - works well on a static structure and can also be
combined with MD simulations - thermodynamic approach.
c) Other thermodynamic approaches - please see : Rasaiah et al. Ann. Rev.
Phys. Chem. 2008, 59, 713.

Hope this helps.

ViV

On 18 May 2012 12:46, Wendy González <locuswendy_at_gmail.com> wrote:

> Dear VMD Users:
>
> I would like to calculate the amount of waters enclosed in an internal
> cavity of a protein during MD simulations.
> Do you have any tip?
> Thanks in advance,
> Wendy
> 

-- 
Vivek Sharma, PhD