hello:
I am using the following parameters for lipid 11 FF POPE study:
equilibration
&cntrl
imin=0, irest=1, ntx=5,
nstlim=25000000, dt=0.002,
ntc=2, ntf=2,
cut=10.0, ntb=2, ntp=3, taup=2.0,
ntpr=5000, ntwx=5000, ntwr=50000,
ntt=1,
iwrap=1,
temp0=310.0,
csurften=3, ninterface=2,gamma_ten=26,
/
and I did two test:
1. 50ns for pre-equilibrated POPE (40ns under CHARMM36)
2. 100 ns for protein/POPE (POPE also equilibrated for 40ns under CHARMM36)
what I found is that for both cases, the POPE are too 'ordered' and it
has some preference for origination. Does any body have any idea what
happen to those lipids.
here are three screenshot from VMD for above mentions.
https://dl.dropbox.com/u/56271062/f/1.jpg
https://dl.dropbox.com/u/56271062/f/2a.jpg
https://dl.dropbox.com/u/56271062/f/2b.jpg
BTW, does anybody knows how to calculate area/lipids in Amber so that we
know whether our system is reliable or not?
thank you very much
Albert
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 18 2012 - 07:30:03 PDT
