AW: Energy minimization of membrane

From: Norman Geist (
Date: Fri Feb 03 2012 - 01:14:50 CST



I'm not a specialist in bio chemistry, more on IT, but I would expect your
membrane as not big enough to be realistic without its periodic copys. So it
won't behave good, as it would be in vacuum, and the best energy
conformation achieved then, wouldn't be the one you want. I would expect
that it will relax more into a strange conformation, as in a realistic one.
Also, if you don't set PBC, your solvent will diffuse away, if there is one.


What's the reason for not want to set PBC in minimization? If you want to
look if your system want to expand, you can try that out with some different
box sizes, and with dynamics, not minimization as minimization will not move
the system much.


Correct me if required ;)


Best wishes


Norman Geist.


Von: [] Im Auftrag
von Boyang Wang
Gesendet: Freitag, 3. Februar 2012 06:31
An: R. Charbel Maroun
Betreff: Re: namd-l: Energy minimization of membrane


Hi Charbel,


I think PBC is necessary, but keep in mind that calculations will be much





On Thu, Feb 2, 2012 at 8:37 PM, R. Charbel Maroun <>


When we do energy minimization with NAMD of a protein-membrane system,
do we have to give PBC in the script, just like for a
molecular dynamics calculation or is this implicitely taken into
consideration? If not, that means that the protein-membrane system is
in vacuum and could become unstable during minimization.


C Maroun

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Boyang Wang, Ph.D.

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