From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sat Jun 27 2015 - 19:36:17 CDT
Hi Kevin,
They do what they say on the tin. useFlexibleCell makes the unit cell
flexible. The default arrangement for pressure control (with flexible
cell off) changes the unit cell isotropically, useFlexibleCell decouples
the three axes, so that the box can change dimensions independently. For
membrane simulations, this is insufficient, as for sufficiently long
simulations, you may get a squished membrane, as x may shrink and y may
grow stochastically (or vice versa), and electrostatic contacts between
the protein may reinforce this trend. useConstantRatio fixes the x and y
axis so that they grow and shrink together, so your membrane protein
doesn't contact itself. I am unfamiliar with how precisely its
implemented, but I do know that I've gotten nonsense trajectories when I
was learning and did not include those options for membrane protein
systems that I got a very non-square shape for the membrane given enough
time.
-Josh
On 6/26/15 11:32 PM, Kevin C Chan wrote:
> *Dear Users,*
> *
> *
> *I am a bit confused when to turn on “useFlexibleCell” and
> “useConstantRatio” options for simulations of systems which contain
> membrane (or even proteins on/inside the membrane). As the NAMD manual
> gives relatively brief descriptions, I would like to hear some
> experience sharing on this. I am interested in whether the option
> would affect any physical results and how NAMD actually achieve such
> constant ratio or area (of a membrane I guess?). *
> *
> *
> *Thanks in advance,*
> *Kevin*
> *City University of Hong Kong*
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