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

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 22 15:04:35 CET 2003

On Wed, 2003-01-22 at 12:09, Francesco Tordini wrote:
> Thank you David for your advice. Now I've created two distinct files 
> for position restraint for dppc and dppe. It seems to work.
> I've tried to make an energy minimization on my system, and in fact
> I find the new energy contributions for position restraint.
> 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's probably just periodic boundary conditions. Your molecule is stored
as a single contiguous piece, so that those molecules on the boreder of
the box have to stick out somewhere. You will find a dent on the
opposing side.
> Cheers
> Franz
> =====================================================================
> Dr. Francesco Tordini
> Università di Milano-Bicocca
> P.zza della Scienza, 1
> 20126 Milano
> tel.  0264483473
> cell. 3282794451
> email tordini at tiscalinet.it
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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