[gmx-users] Entending water in negative Z direction

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Jun 4 21:36:34 CEST 2009

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.


-- original message --


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.


  Anirban Ghosh

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