[gmx-users] question about image?

David spoel at xray.bmc.uu.se
Thu Feb 12 21:00:01 CET 2004

On Thu, 2004-02-12 at 20:54, Weihua Guo wrote:
> Hi, 
> My system has two peptides surrounded by water
> molecules. Will the two peptides be imaged seperatedly
> or as a whole during mdrun? I would like them to be
> imaged as a whole, but hope that it wouldn't make
> later analysis harder (I would like to study the
> interactions between the two peptides, e.g. H-bonds at
> the interface etc.). Could someone provide some
> suggestions?

imaging is per molecule, but all analysis programs take this into
account. furthermore you can use trjconv -cluster to make a trajectory
in which the molecules have their shortest intermolecular distance.
> Thanks.
> Weihua Guo
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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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