> After MD using Amber when i reimage the files i find there are three layers
> hexane/water/ hexane...
With periodic imaging this is likely not an issue and is expected as
there is nothing to prevent the layers from diffusing in space. To avoid
it and keep the layer somewhat fixed in space would require restraints
(which is likely not desirable).
> trajin md1.mdcrd
> trajin md2.mdcrd
> trajout reimage.mdcrd
> center :1101-1191
> image center familiar
> rms first out wt1mg_eq_rms.out
>
> i am unable to find where am i wrong??
Likely nothing is wrong. If you want to "see" the periodic images to make
sure layers are as you expect (without vacuum bubbles and contiguous in
space), you could build up some snapshots from a series of ptraj runs to
highlight the periodic system with visualization of the unit cell and its
first set of nearby images.... Pick a later frame from your trajectory,
say frame 1000, then build_crystal.csh "md2.mdcrd 1000 1000 1" (assuming
the prmtop is named "prmtop").
A csh script (build_crystal.csh):
#!/bin/csh -f
set rst = $1
foreach x (0 1 2)
foreach y ( 0 1 2)
foreach z ( 0 1 2 )
ptraj prmtop <<EOF
trajin $rst
trajout img_$x$y$z.pdb pdb
#strip :WAT
center :1101-1191
image xoffset $x yoffset $y zoffset $z
EOF
mv img_$x$y$z.pdb.1 img_$x$y$z.pdb
end
end
end
--tec3
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Received on Fri Sep 16 2011 - 06:30:05 PDT
