Re: Mail reg Parameter file

From: Fotis Baltoumas (
Date: Mon Apr 20 2015 - 08:48:36 CDT


First of all, you misunderstood what the tutorial said. The NBFIX
parameters are NOT for keeping any part of the lipids fixed, they contain
corrections for non-bonded interactions between carbonyls and ions,
appearing under the respective CHARMM field (i.e. NBFIX). These new
parameters are already part of the CHARMM36 force field so you probably
need nothing else than the standard protein and lipid C36 parameters (for
more parameters concerning ions and their interactions, check the toppar
stream files (*.str) in the CHARMM36 ff package in MacKerrell's website,
if the need arises).

Fixing the position of atoms is done through the fixedAtoms options, in
the manner described in the tutorial, i.e. generating a reference file in
which atoms that are to be kept fixed have a beta value of 1 while all
moving atoms have a beta of 0, and adding the following lines to your NAMD
configuration file:

fixedAtoms on ;#enabling the fixing of specific atoms
fixedAtomsFile fixedatoms.pdb ;#the pdb containing the info on what is fixed
fixedAtomsCol B ;# which column contains the info in the fixedatoms file
fixedAtomsForces on ;#whether these atoms participate in calculations

Finally (and this is important so you don't waste your time for no reason)
it is the lipid head groups that need to be fixed for the equilibration of
a membrane, not the tails. You want the tails to move freely, so that you
can "melt" them and induce the disordered state of a fluid-like membrane.

I would suggest you first try a few simulation examples and
experimentations with the tutorial, so that you get more familiar with how
membrane simulations work, before you try anything else.


> Dear Namd User
>                          I would like to run  Memebrane Simulation in Namd
> 2.9 using par_all36_prot_lipidNBFIX.prm ( to keep tails of lipid fixed)
> But Tutorial contains  only par_all27_prot_lipidNBFIX.prm  So where coud i
> Get such file ?
> . Thanks in Advance

Fotis A. Baltoumas
Ph.D. Candidate
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
email :

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