summary: lipid bilayer MD simulations

From: Xavier Deupi <>
Date: Fri 16 Mar 2001 04:01:46 -0800

Hi all,

first of all, thank you to all the people who answerd. Here I report a
short summary of the answers.

I have received some refferences from Pornthep Sompornpisut:

        - Smondyrev AM, Berkowitz ML: United atom force field for
        phospholipid membranes: constant pressure molecular dynamics
        simulation of dipalmitoylphosphatidylcholine/water system.
        J Comput Chem 1999, 20:531-545.

        - Lucy R Forrest and Mark SP Sansom, Cur.Op.Str.Bio. 2000, 10:174

        - Kenneth M Merz Jr:Molecular dynamics simulations of lipid bilayers.
        Cur.Op.Str.Bio. 1997, 7:511

In addition, I have received some advices about the use of united-atom
force fields

        From: Bill Ross <ross_at_cgl.ucsf.EDU>

        If you use united-atom be careful with improper torsions, because
        I was unable to get leap's method of applying them to work with
        the canonical united-atom ff. This is because the old prep way
        allowed you to specify the order of the three atoms; with leap
        the order is arbitrary (based on atom name or type, I forget which),
        and this doesn't work when the improper is not planar.
        (Bill Ross posted some additional information about this
        point directly to the list)

        From: Peter Kollman <pak_at_cgl.ucsf.EDU>

        Using united vs all atom depends on the resolution of
        the question you want to ask...if it is ligand binding to an
        active site, all atom is advised...but if you want a general
        environment of lipids united atom is likely to suffice...

And there were some messages posted to the list by Thomas Huber, Anita
Ilze Zvaigzne and Mihaly Mezei about mixing parameters from different




  Xavier Deupi
  Computational Medicine Lab
  Biostatistics Unit. School of Medicine
  Universitat Autonoma de Barcelona. CATALUNYA (Spain)
  Phone : (3493)-581.23.48
Received on Fri Mar 16 2001 - 04:01:46 PST
Custom Search