From: Basak Isin (isinbasak_at_yahoo.com)
Date: Thu Jun 10 2010 - 18:18:03 CDT
These can help solving your problem:
1. Fixing everything in the system including the lipid head groups and then minimizing and equilibrating the tail of the lipids as described in the membrane tutorial. This will relax the tails around your protein.
2. Starting the simulations at a low temperature and gradually increasing it.
3. Increasing the margin (you can make it 3).
4. If nothing else works, you can use membranes that are already well equilibrated. There are some deposited at Peter Tieleman's website (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) but these are very short equilibrations and these lipids are for Gromacs and converting them to the NAMD format might be cumbersome. There might be other places to download equilibrated lipids.
0.1 fs is too short for step size.
Note: I tried sending another email previously but my browser froze so you might have gotten a similar email before :o).
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From: Ale Gomez <agomez.fisica_at_epn.edu.ec>
Sent: Thu, June 10, 2010 6:22:33 AM
Subject: namd-l: Protein in a Lipid Membrane
I am working on a system with a protein in a lipid membrane. My system has almost 40 thousand atoms and measures 75X75. I had a lot of problems preparing the equilibration conf file because it doesn't run (my system became unstable or has atoms moving too fast) unless I use the following parameters:
# Force-Field Parameters
# Integrator Parameters
timestep 0.1 ;# 2fs/step
rigidBonds none ;# needed for 2fs steps
Comparing with the parameters in membrane tutorial (available in NAMD website), my numbers are bigger and I do not know if these are correct. Could any one help me with this predicament??.
Thanks in advance!!.
Biophysics and Molecular Modeling Group
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
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