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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 12 2015 - 23:30:02 PDT
