[gmx-users] Problem in energy minimization for a empty membrane system

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jun 24 08:02:19 CEST 2009

Bing Bing wrote:
> Hi!
> Thanks for your suggestion on the tutorial. I will try it out.
> I actually tried to use the starting structure without going through 
> editconf and alteration but it failed. Here's the error:
> ERROR: The cut-off length is longer than half the shortest box vector or 
> longer than the smallest box diagonal element. Increase the box size or 
> decrease rlist.
> I've tried on reducing the rlist but still failed. Please advice.

There's a reason for the editconf step. The size of the box is encoded 
in the coordinate file, and needs to be large enough both for your 
system and your model physics. You should not be meddling with your 
model physics (i.e. rlist) unless you know what you're doing :-)

> According to the tutorial you suggested, we are suppose to use genbox to 
> solvate the membrane and remove those water manually by script that go 
> inside the membrane. Does this mean that I'm suppose to throw away the 
> water from the starting structure and resolvate it again?

Probably. Water is the easiest thing to generate, so it's the easiest 
thing to remove to simplify things.


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