Perhaps a silly question: Are you sure, you only divide the xy area by the
number of lipids in one leaflet (i.e. Not the total amount of lipids)?
Sarah
Den 29/06/12 14.52 skrev "Vlad Cojocaru"
<vlad.cojocaru.mpi-muenster.mpg.de>:
>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
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>--
>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
>
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 29 2012 - 06:00:05 PDT
