From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon May 13 2013 - 00:22:55 CDT
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.
> -----Urspr¨¹ngliche 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,
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