Re: Periodic boundary condition in a membrane simulation

From: Axel Kohlmeyer (
Date: Mon Feb 09 2009 - 19:29:40 CST

On Mon, 9 Feb 2009, Nd S wrote:

NS> Eric,
NS> To visualize periodic cells, on the TKCon Console (Extensions Menu) type
NS> molinfo top set a length_in_x
NS> molinfo top set a length_in_y
NS> molinfo top set a length_in_z

but this is not correct.

the cell lengths are 'a', 'b', and 'c'.

please note, that namd2.6 generated .dcd files should
already contain the cell dimension information and VMD
will read id.

the most convenient (and safest) way to re-set the cell
information is to use the pbctools commands, i.e.

pbc set {102.7 101 83.5}

NS> > After a short md run, the lipid molecules on the side start to flip
NS> > randomly which is a sign of no contact with other lipid in the neighboring
NS> > cells. I wonder if the way I set up the PBC is wrong. In addition, I wonder
NS> > if there is a way to visualize the periodic cells (with VMD preferably)? Any
NS> > suggestions will be appreciated. Thank you.

"pbc box" will allow you draw a box indicating you current cell
dimensions and then with "pbc wrap" and the corresponding flags,
you can wrap coordinates back into the principal unit cell.

check out the details of the pbctools documentation (very detailed
and worth a look).


NS> >
NS> >
NS> > Eric
NS> >
NS> >
NS> >

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:20 CST