If you are using PBC, extending the positive direction *is* extending
the negative direction, they are the same thing. If you really must
center your bilayer on Z, then try editconf -translate 0 0 N
And please take this only as a useful suggestion, but simulating a
GPCR in a membrane protein before fully understanding PBC is probably
the wrong order to go about things. You might save yourself a heap of
time in the end by starting with some simpler systems first.
Chris.
-- original message --
Hi ALL,
In previous posts I mentioned the problem I am facing: a portion of my
protein (GPCR in a POPC bilayer) in extending out of the water box in
negative Z-direction, how to extend the water in that direction. I
have gone through the PBC section of the manual. While changing the Z
coordinate value of the last line of the .gro file I am able to extend
the water layer in the positive Z direction. But I am not able to
extend it in the opposite direction. Decreasing the Z coordinate value
is not helping that. How to do this? Any suggestion is welcome.
Regards,
Anirban Ghosh
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