Hi Albert,
Your gamma_ten value is very high, and I think that is the problem. The gamma_ten
value specifies the surface tension in dynes/cm/interface, which means that you've
specified a value of 60 dynes/cm/monolayer (120 dynes/cm for the whole bilayer).
I'm guessing the bilayer is extended too much in the xy dimension and becomes
compressed in the z dimension. Try with a much lower gamma_ten. We ran POPE
at a range of surface tensions and found that gamma_ten=26 (=> 26 dynes/cm/leaflet)
was the best value. We hope to optimize the force field, so that membrane simulations
in AMBER eventually can be run in the tensionless NPT ensemble.
Best regards,
Åge Skjevik
> Date: Mon, 14 May 2012 08:49:44 +0200
> From: mailmd2011.gmail.com
> To: amber.ambermd.org
> Subject: [AMBER] bi-layer membrane system shrink with NPgamaT
>
> Dear:
>
> I am testing the latest lipids 11 FF with NPgamaT and I found that
> my POPE shrinked with NPgamaT. here is one of my NPgamaT input file
>
> equilibration
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=1000000, dt=0.002,
> ntc=2, ntf=2,
> cut=10.0, ntb=2, ntp=3, taup=2.0,
> ntpr=5000, ntwx=5000, ntwr=50000,
> ntt=1,
> iwrap=1,
> temp0=310.0,
> csurften=3, ninterface=2, gamma_ten=60,
> restraintmask=':PE &!.H, 1-311 &!.H',
> restraint_wt=50.0
> /
>
> the harmonic restrain on POPE head and protein was stripped off from
> 50-->0 gradually over 20 ns (with 12 input file). However, at the end of
> equiliration, I found that bi-layer lipids shrink ed dramatically: I
> only saw one layer lipids and the original bi-layer crossed with two
> each other....
>
> Does anybody have any idea for this?
>
> thank you very much
>
> BEST
> Albert
>
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Received on Mon May 14 2012 - 01:00:02 PDT
