Hi,
I did use a frcmod file to change the parameters. But Amber use additive
mean for sigma and geometric mean for epsilon, while I need to use geometric
mean for both sigma and epsilon to get the right parameter for NaCl. This is
the reason why I also need to change prmtop file after generate one.
Thanks.
Jianhui
On Sun, Jan 17, 2010 at 2:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Sun, Jan 17, 2010 at 12:07 PM, Jianhui Tian <jianhuitian.gmail.com>
> wrote:
> > Hi all,
> >
> > I am now trying to do simulations with ions parameters from Chen et al
> (J.
> > Phys. Chem. B 2007, 111, 11884-11887) and ffamber99sb together. After
> > generate the prmtop file, I need to identify the Lennard-Jones parameters
> > for NaCl and change them accordingly. I have read the prmtop format and
>
> I believe you can do this directly in leap using an frcmod file.
> There is no need to create the prmtop and edit it by hand. The only
> thing you'll want to make sure is that all units are consistent, but
> they should be well-documented for amber.
>
>
> Good luck!
> Jason
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Sun Jan 17 2010 - 12:30:03 PST
