[gmx-users] Re: Hbonds - Res - Ligand

Steven Neumann s.neumann08 at gmail.com
Fri Oct 28 15:45:59 CEST 2011

With other residues is the same... and changes are bigger. Which trajectory
in this case is reliable?

My wsteps in trjconv involves:

1.      First make your molecules whole if you want them whole (system).

3.      Extract the first frame from the trajectory as reference for
removing jumps if you want to remove jumps.

4.      Remove jumps if you want to have them removed using the first frame

5.      Center your system using some criterion. Doing so shifts the system,
so don't use trjconv -pbc nojump after this step.

6.      Put everything in some box.

7.      Fit if desired and don't use any PBC related option afterwards.

On Fri, Oct 28, 2011 at 2:28 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Dear Gmx Users,
> I have compared average number of hbonds per time frame between my ligand
> and protein:
> 1) Using trajectory obtained straight after simulations:
> g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg
> Avergage number of hbonds: 0.146
> 2) Using trajectory modified by trjconv according to the PBC workflow on
> www.gromcacs.org :
> g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num
> 91withLigandsHbond.xvg
> Avergage number of hbonds: 0.156
> Does anyone know why this value changed and I obtained slightly different
> results?
> Thank you,
> Steven
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