Hi Albert,
One would expect a protein integrated into the bilayer to have an effect on the
lipids and vice versa. The experimental value we've used is for a pure POPE
bilayer (Rappolt et al, Biophys J, 84, 3111-3122, 2003). I'm not sure what
would be a reasonable value for the membrane/protein system.
Best regards,
Åge
Date: Fri, 29 Jun 2012 16:16:46 +0200
From: mailmd2011.gmail.com
To: amber.ambermd.org
Subject: Re: [AMBER] update for POPE test
Hello Age:
thank you for kind comments. I see that I calculate the bilayer for
all lipids. Then we have to multiple 2 for original plot. here is the
new case for a protein in POPE lipids plot. I use the same command as
you indicated in last thread to generate new informations.
in this case, area/lipids is around 68 which is a little bit higher
than experimental data.....
best
Albert
On 06/29/2012 02:56 PM, Åge Skjevik wrote:
>
> Hi Albert,
>
> Firstly, I generally include all the atoms in the box in the vector command:
> vector x * box out filename
>
> Also, I can't get your information to add up. Your mask for the lipids (:314-679)
> indicate that you have 122 lipids in your system and not 126. My guess is that
> you have 122 (or 126) lipids in total in your bilayer. To calculate the area per lipid,
> you have to divide by the number of lipids per monolayer (which would be 61 or 63
> in your case?).
>
> Best regards,
>
> Åge
>
>
> Date: Fri, 29 Jun 2012 14:32:16 +0200
> From: mailmd2011.gmail.com
> To: amber.ambermd.org
> Subject: [AMBER] update for POPE test
>
>
>
> hello guys:
> here is my test for POPE based on the latest lipid 11 FF. I am
> using the following ptraj.in for analysis:
>
> trajin md.mdcrd 1 50000 10
> vector POPE :314-679 box out pope.vector
>
> here is the output file:
>
> # FORMAT: frame vx vy vz cx cy cz cx+vx cy+vy cz+vz
> # FORMAT where v? is vector, c? is center of mass...
> 1 63.9490 63.9490 91.6050 0.0000 0.0000 0.0000 63.9490
> 63.9490 91.6050
> 2 64.0190 64.0190 91.5460 0.0000 0.0000 0.0000 64.0190
> 64.0190 91.5460
> 3 64.1090 64.1090 91.2790 0.0000 0.0000 0.0000 64.1090
> 64.1090 91.2790
>
> I use X multiple Y and divide my lipids number (126 total in all). I've
> run two MD, one is 50 ns for POPE itself; the second is protein in
> pre-equilibrated POPE (CHARMM 36 FF 50 ns). here is md.in for production:
>
> production dynamics
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=50000000, dt=0.002,
> ntc=2, ntf=2,
> cut=10.0, ntb=2, ntp=3, taup=2.0,
> ntpr=1000, ntwx=1000, ntwr=50000,
> ntt=1,
> iwrap=1,
> temp0=310.0,
> csurften=3, ninterface=2,gamma_ten=26,
> /
>
> enclosed this email, you can find a plot for both cases. It seems that
> the area/lipids is far from the plot Ross provides. Does anybody have
> any idea what's going on?
>
> thank you very much
> Best
> Albert
>
>
>
>
>
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Received on Fri Jun 29 2012 - 08:00:03 PDT
