[gmx-users] Re: Problem with restraint in lipid membrane

[Anton Feenstra]

Francesco Tordini wrote:
> 
> What is still unclear it is that the structure
> observed as a result of minimization shows some chains that are located
> out of the box boundaries. I get the same result with the original
> dppc64.pdb file and also with molecular dynamics.
> My question is: is this problem anyway related to the following
> entry in log file:
> 
> "Removing pbc first time
>  Done rmpbc"
> 
> What this expression means?
> Maybe it's a trivial question, but i'm quite a beginner with gromacs

It is a normal consequence of the periodic boundary conditions (pbc).
mdrun will always produce 'whole' molecules, and will keep the first 
atom of a molecule inside the box. All the rest of the molecule could
be sticking out. It doesn't matter, since the system is periodic, and
it is simply a matter of choice how to treat this. It might look very
funny indeed, and can sometimes be confusing.

I have just today submitted a change to trjconv which will put the
*center of mass* of all residues (note: residues, not molecules, 
since that requires knowledge of the topology and is much more work
to program) back into the box.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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|        | Python)                                                   |
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