From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jun 07 2013 - 20:56:46 CDT
it will have zero impact on your simulation, it's just a visualization
issue. There are a number of emails in the thread about re-centering a
trajectory for visualization.
As to why it happens, certainly part of it is just diffusion, but why does
it continually drift in the same direction? Maybe it isn't fully
equilibrated/minimized and some clash gives it some initial momentum. What
thermostat are you using? Also, you can initially restrain the lipids and
equilibrate the water around it then release that constraint. This may
help if you are very concerned with the drift, but the position of the
periodic boundary is arbitrary.
On Fri, Jun 7, 2013 at 9:36 PM, 翁林岽 <wenglindong_at_yahoo.com.cn> wrote:
> Hi, all,
> When I equilibrate a DPPC/water system, the center of the lipid bilayer
> always shifts by several Ås along the Z axis. Since the center of the
> simulation box is kept at (0, 0, 0), the consequence is that 1) the water
> layer on one side is squeezed into the neighbor periodical box and
> gradually shrinks and 2) the water layer on the other side correspondingly
> becomes thicker due to the periodical conditions I think. As the
> equilibration goes on, the shrinking water layer becomes a very thin layer.
> Does anyone observe the same problem in your simulation?
> I am afraid that the lipid bilayer may eventually be seperated by the
> periodical boundary so that the original water<--->lipid bilayer<--->water
> complex will become a lipid monolayer<--->water<--->lipid monolayer one in
> the simulation box. Probably, with periodical conditions, such changes will
> not negatively affect the simulation accuracy. But can anyone tell me why
> there is such shift? Are these changes normal or acceptable? Are there any
> ways we can avoid such shifts and make the simulation box look normal?
> Any suggestions would be really appreciated.
> UNC Charlotte
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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