Steven Neumann wrote:
Hi Justin,
Do you have any clue of this problem? You are the last hope, please help :)
Sorry, I have no idea. If I did, I would have posted earlier. In principle,
PBC re-imaging should not affect the calculation of distances and angles needed
by g_hbond and I have never seen such an outcome.
-Justin
Steven
On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> 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 <http://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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
