flexiblecell and constant ratio

From: regafan_at_usc.es
Date: Fri Feb 02 2007 - 06:09:00 CST

Hello,
I am doing MD simulations of membranes of different compositions using
NAMD, and I am a bit confusing about the use of flexible cell and
constant ratio. I did the equilibration and production step at NPT
conditions, using

UsegroupPressure yes
UseFlexibleCell yes
UseconstantRatio yes
langevinPiston on
langevinPistonTarget 1,01325
langevinPistonPeriod 200
langevinPistonDecay 200
langevinPistonTemp 310

and I did also another simulation using

UsegroupPressure yes
UseFlexibleCell no
UseconstantRatio no
langevinPiston on
langevinPistonTarget 1,01325
langevinPistonPeriod 200
langevinPistonDecay 200
langevinPistonTemp 310

The difference between the results of both simulations are very big,
for example the thickness of the membrane varies a lot. Which
condition (flexiblecell yes/no) do you think is better for simulating
membranes. What is the advantage or disadvantage of using flexiblecell
and constant ratio?

Another question is about constanRatio. In the NAMD manual indicates
that it maintains constant shape in first two cell dimensions, this is
x and y. What happens if my z dimension does not correspond to the
direction of the thickness of the membrane? Is constant ratio not
recommended in this case?

I hope you can help me. Thanks a lot!

Rebeca.
regafan_at_usc.es

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