[gmx-users] g_rms and pbc

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 24 22:24:01 CET 2004

On Wed, 24 Mar 2004, Alan Wilter Sousa da Silva wrote:

>Hi List!
>I'm facing a really boring problem. I have a MD in which system (protein
>with 2 chains plus drug) cross box appearing in the other side, perfectly
>normal according to PBC.  However, calculating g_rms with options -prev 1
>and -nopbc I still got peaks in my rms plot, evidencing it's not
>neglecting PBC.
trjconv -pbc cluster

>Please how am I supposed to be wrong in my procedure?

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 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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