From: Axel Kohlmeyer (
Date: Thu Jul 16 2009 - 11:56:57 CDT

On Thu, 2009-07-16 at 15:06 +0800, yzliu wrote:
> Dear all,
> I have simulated a membrane system with NAMD.
> And I want to calculate the sasa of each lipid with
> the command "measure" in VMD.
> But first of all, the PBC must be used to reduce edge
> effect. My idea is replicating the cell 3 * 3 times in
> the xy plane to a big box. Only the central image of
> the replicated system is used for analysis.
> My problem is how to replicate the cell in my trajectories.

that can be done with some scripting, but could be quite
memory and time consuming.

to get converged numbers, you'll have to compute the
SASA over a patch anyways and then divide by the number
of lipids and average this over a sufficiently long
trajectory. so i'd propose a simple solution.

- if your trajectory does not wrap atoms/residues
  use pbctools (pbc wrap) to wrap all lipids back
  into the principal unit cell
- measure the SASA for a patch that leaves out an
  adequate "rim". you'll have to use the restrict
  option, to get the proper result, IIRC.
- adjust for number of lipids in the restricted
  area and average over the trajectory.

that should give you effectively the same result
at much less effort, IMO.


> Thanks in advanced.
> Regards,
> Yingzhe
> --
> ==============================
> Yingzhe Liu
> PHD Student of Analytical Chemistry
> Chemistry Department
> Nankai University
> Tianjin, P.R.China,30071
> Email:
> ==============================

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.