[gmx-users] Creating a layer bigger than one PBC
feenstra at chem.vu.nl
Mon May 12 14:23:01 CEST 2003
> genconf can be used in individual frames.
> then you still have to cut out afterwards, but that is probably easiest.
Not if you want to keep whole molecules.
I've run into this when wanting/needing to extend or contract water
boxes, keeping the water around the protein and creating as little
disturbance in the whole system as possible. It'd be nice to have a
tool that could do this automatically, perhaps it could be an option
in genbox or genconf.
Meanwhile, what should work is the following:
1) use genbox -box to 'multiply' your original system. genbox has
the advantage over genconf in that it will truncate your new system
on the desired box size, and keep whole molecules.
2) if desired, re-center your protein with editconf, don't worry
about lipids shifting out of the box, mdrun will take care of that,
otherwise you can use trjconv to do that.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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