VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon May 15 2006 - 13:44:00 CDT

On Mon, 15 May 2006, John Stone wrote:

JS>
JS> Hi,
JS> I hadn't heard about this previously, I'll have to have a look
JS> and see what's going on there. Not much has changed with that plugin
JS> since Ilya originally wrote it, so hopefully this is easy to fix.

may i add one more observation here.
there also is a limit if you want to go to larger membranes
from within the membrane builder tool. as soon as the number
of Wxx segments goes beyond 99 the code will choke. see:

Info: generating structure...
Info: segment complete.
building segment W99
disabling angle autogeneration
disabling dihedral autogeneration
Info: generating structure...
Info: segment complete.
building segment W100
duplicate segment key W100

just try to build a 200x200 membrane to reproduce it (this is
with the latest CVS code, btw). looks like a format issue
somewhere, since the Lxxx segments labels can be larger than 99.

cheers,
    axel.

JS>
JS> John Stone
JS> vmd_at_ks.uiuc.edu
JS>
JS> On Thu, May 11, 2006 at 11:47:11AM -0700, Ting Wang wrote:
JS> >
JS> > Dear VMD users,
JS> >
JS> > It seems there is a bug in the Membrane Plugin.
JS> >
JS> > When the membrane size is larger than 50A x 50A, the commond "membrane -l
JS> > popc ..." will generate lipid molecules with serious clash. Some atom-atom
JS> > distances are even smaller than 0.2A.Energy minimization can not get over
JS> > it, actually minimiztion can not run.
JS> >
JS> > Did anybody else notice this? Can this bug be fixed?
JS> >
JS> > Thank you very much!
JS> >
JS> > Ting
JS>
JS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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.