Hello Albert,
50ns may not be long enough to converge just your POPE bilayer. Are you able to show the area per lipid vs. time for your simulation?
The first screenshot qualitatively looks too ordered. But I can't tell with the second and third.
Are you actually calculating an order parameter for your acyl tails? It's fairly common to compare this to experimental order parameter values.
Please see my previous comments about the overly ordered saturated acyl chains in Lipid11.
It is possible to extract area per lipid using ptraj. There is a command 'vector' that will output the periodic box dimensions.
Also, surely the protein and the relative number of lipids will play a role in your membrane bound protein system.
Ben
Walker Molecular Dynamics Lab
On Jun 18, 2012, at 7:10, "Albert" <mailmd2011.gmail.com> wrote:
>
> 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
>
>
>
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Received on Mon Jun 18 2012 - 09:30:02 PDT
