Hi amber users,
I have a ptraj image problem after I have checked the previous archive of
amber mail-list.
My system is a small molecule (resid: 1) merged in lipid bilayer (resid:
2-69, in which 2-35 is one layer, and 36-69 is another layer) in rectangular
parallelepiped water box. In the z-direction, the original organization of
each layer is "W1--L1--L2--W2", where "W" means water and "L1 (or L2)" means
one layer of lipid. I have tried different protocols to do the image.
However, sometimes I can find "L2--W2--W1--L1" organization of the system in
the whole trajectory.
(1)
trajin mdcrd
center :1-69 mass origin
image origin center familiar
trajout newtraj netcdf
****
(2)
trajin mdcrd
center :2-35 mass origin
image origin center familiar
center :1-69 mass origin
image origin center familiar
trajout newtraj netcdf
Can anyone help to figure out the problem? Thanks in advance.
Best,
Hao
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Received on Thu Jan 20 2011 - 07:30:05 PST
