From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Feb 02 2007 - 09:26:48 CST
If you're using a membrane you almost certainly want to use either
UseconstantRatio or useConstantArea (I tend to prefer the former). If
you use the configuration in your second example variations in size
along the mebrane's plane will be treated as identical to variations in
the solvent direction, which is almost certainly not what you want.
If you z direction doesn't correspond with the thickness of the
membrane, the best solution is probably rotating your system 90 degrees
;-). Otherwise useConstantRatio is likely to behave oddly.
Peter
regafan_at_usc.es wrote:
> 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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