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 - 06:00:05 PDT
