[gmx-users] (no subject)

[Anton Feenstra]

J Lorieau wrote:
> 
> Hi Anton,
> 
>         Molecules are suppose to diffuse. It wouldn't be a problem in my
> simulation if I had a very big box. However, my HIV protease drift right
> out of the box. This causes it to drift out of the solvent, and it
> causes one of the sub-units to fly to the other side of the box - which
> rips my protein apart. I've tried comm_mode=linear, but it doesn't work.

That's not true. You have PBC, hence the subunits that appear to
be separated are in fact still together. Wait for it to diffuse 
further and the second subunit will 'join' the first again on the
other side. (It might be inconvenient for viewing, though.)

In principle 'trjconv -pbc nojump' should keep your subunits together,
but I hear from several people on the list that this appears to be
broken. I have no good test-systems to look into this, but maybe
someone else could?
-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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