From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon May 13 2013 - 03:17:29 CDT
Hi Lina,
The question to be asking yourself now is: what kind of boundary conditions do you want for your simulation?
Once you tell us that, we may be able to help you achieve it.
Jerome
----- Original Message -----
> Hi,
>
> You can define whatever box shape you want, when building and
> solvating your
> molecular system. From there on, you can run it with NAMD without
> defining a
> periodic box at all. Means no CellBasisVector parameters. This will
> run the
> simulation without periodic boundary conditions, as there's no need
> and
> reason to define a box in that case. Remember that PME needs pbc, so
> you may
> be interested in "fulldirect" to keep the long range electrostatics
> and not
> doing cutoff electrostatics.
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von ???
> > Gesendet: Donnerstag, 9. Mai 2013 10:50
> > An: namd-l_at_ks.uiuc.edu
> > Betreff: namd-l: Can I define a simulation box but turn off the PBC
> > at
> > the same time?
> >
> > Dear all,
> >
> >
> > Can I simulate a SMD system in a defined rectangular
> > parallelepiped
> > box, but turn off the periodic boundary condition? How to realize
> > this
> > function using NAMD?
> >
> > Thank you for your help and suggestions in advanced!
> >
> >
> > Best regards,
> >
> > Lina
> >
> >
> >
>
>
>
>
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