[AMBER] update for POPE test

From: Albert <mailmd2011.gmail.com>
Date: Fri, 29 Jun 2012 14:32:16 +0200

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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pope_plot.jpg
(image/jpeg attachment: pope_plot.jpg)

Received on Fri Jun 29 2012 - 06:00:04 PDT
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