[gmx-users] problem with trjconv

David spoel at xray.bmc.uu.se
Wed Aug 10 16:23:14 CEST 2005

On Wed, 2005-08-10 at 16:12 +0200, Jozef Hritz wrote:
> 	Gromacs Users,
> I have MD trajectory of protein dimmer. I have observed different behavior
> of its monomeric units (they are structuraly identical, composed from
> 2065 atoms). Therefore I wanted to superimposed the second monomeric unit
> to the first one and then to observe, where are the biggest structural
> differences.
> I have wrote [ monomer_1 ] and [ monomer_2 ] groups with corresponding 
> atoms into index.ndx file and then I had run trjconv
> For the initial structure:
> trjconv -f first.gro -o monomer_2.gro -s run.tpr -n index.ndx -fit
> rot+trans
This will take the structure in first.gro and superimpose it on the one
in fit.tpr. Is that what you intend to do?

You can also use
> For least squares fit I have used group [ monomer_1 ] and for output group
> [ monomer_2 ]. When I have checked the output, there was no fit done. It
> just took monomer_2 part from initial structure first.gro without fiting.
> In the second step I wanted to fit monomer_2 part to monomer_1 during
> whole MD trajectory, but as I wrote I have even problem with the first
> frame.
> Can anybody help me with this problem?  
> Thank You
> Jozef
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David van der Spoel, PhD, Assoc. 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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