Hi Justin, Do you have any clue of this problem? You are the last hope, please help :)
Steven On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > 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.neuman...@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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