Re: Protein in a Lipid Membrane

From: Basak Isin (
Date: Thu Jun 10 2010 - 18:18:03 CDT

Hello Ale, 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 ( 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. Good luck, Basak Note: I tried sending another email previously but my browser froze so you might have gotten a similar email before :o). Basak Isin ABOVE ALL NATIONS IS HUMANITY. "What matters - all that matters, really - is the will to happiness, a kind of enormous, ever-present consciousness. The rest - women, art, success - is nothing but excuses." - Albert Camus Cause life is meant for living. Yaki-da ;o) ________________________________ From: Ale Gomez <> To: Sent: Thu, June 10, 2010 6:22:33 AM Subject: namd-l: Protein in a Lipid Membrane Hi everyone 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 exclude scaled1-4 1-4scaling 1.0 cutoff 22. switching on switchdist 18. pairlistdist 24.5 margin 1.5 # Integrator Parameters timestep 0.1 ;# 2fs/step rigidBonds none ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 20 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!!. ------------------------------------------------------------------- Ale Gómez Biophysics and Molecular Modeling Group Physics Department Escuela Politécnica Nacional, Quito - Ecuador Ladrón de Guevara E11-253. Casilla 17-01-1253

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