There must be a mistake here ... How can the area per lipid be around 25 ?
Shouldn't be around 65 or so ??? Even if you get fully ordered lipids,
you'd still have over 50 ...
Vlad
On 06/29/2012 02:32 PM, Albert wrote:
>
>
> 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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--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Fri Jun 29 2012 - 06:00:04 PDT
