On Dec 26, 2012, at 1:12 AM, Vijay Manickam Achari <vjrajamany.yahoo.com> wrote:
> Dear experts,
>
> I am having problem in PBC of my
> bilayer system.
>
> The starting structure of bilayer is as
> below: "O" is lipid head and "|" is lipid tail
>
> OOOOO
> | | | | |
> | | | | |
> OOOOO
> water
> OOOOO
> | | | | |
> | | | | |
> OOOOO
>
> After running production for about 7 ns
> (I notice from VMD) the lipids from top shift to bottom layer as
> below:
>
>
> | | | | |
> OOOOO
> water
> OOOOO
> | | | | |
> | | | | |
> OOOOO
> OOOOO
> | | | | |
>
> The input paramters I am using for
> this production is as blow:
>
> Dynamic Simulation with Constant
> Pressure
> &cntrl
> imin=0,
> irest=1, ntx=5,
> nscm=1000, iwrap=1,
> ntt=3, gamma_ln=2, temp0=300.0,
> ntb=2, ntp=2, pres0=1.0, taup=1.0,
> ntc=2, ntf=2,
> nstlim=100000, dt=0.001,
> ntxo=1, ntwx=500, ntpr=100,
> ntwr=-50000,
> ntwv=-1,ioutfm=1, ntwe=500,
> cut=9
> /
>
> This is like the molecule move upwards
> or the PBC move downwards. In either case, this kind of shift will
> affect my simulation results.
This is merely a visualization artifact and has no bearing on your simulation or the results from it. The variable iwrap=1 is responsible for "wrapping" your bilayers to the other side of the box. However, since there are periodic boundaries, the system is replicated to infinity in every direction. As a result, the monolayer on the top and bottom are actually in a bilayer formation with the corresponding layer in the adjacent periodic cell.
You can use cpptraj and the autoimage command to reimage your trajectory for a more familiar view. You may need to reimage after centering the bilayer system if you want it centered in the water box. See the center and image commands in the manual (and the autoimage command has been discussed many times on this list, so googling autoimage should provide you the information you need.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Dec 26 2012 - 05:30:03 PST
