Thanks Mic.
On Fri, Mar 13, 2015 at 11:42 AM, Michele Bonus <michele.bonus.hhu.de>
wrote:
> Dear Jacob,
>
> the easiest way to do this would be to set the box size to a value which
> gives you slightly more than 2500 water molecules, save the respective
> prmtop and inpcrd files, and then strip off the excess water molecules
> from your prmtop using ParmEd.
>
> Jason Swails provides a good explanation on how to do this here:
> http://archive.ambermd.org/201205/0053.html
>
> Best regards,
> Michele
>
> Am 13.03.2015 um 06:17 schrieb jacob wick:
> > Hi all,
> >
> > I want to set the number of water molecules in the box as 2500. By
> varying
> > the box size I am not able to set the molecules to this accurate value.
> >
> > Is it possible to predefine the number of water molecules in a waterbox
> > around my system of a RNA molecule.
> >
> > Thanks and Regards,
> > Jac
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Received on Fri Mar 13 2015 - 22:30:02 PDT
