Steven Neumann wrote:
On Mon, Jan 30, 2012 at 12:16 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 30/01/2012 8:43 PM, Steven Neumann wrote:
Dear Gmx Users,
I run the simulation of protein with 10 ligands (200 ns). In total
I should have total of 4000 frames as I set up:
nsteps = 100000000
dt = 0.002
nstxout = 25000
... iff the simulation completed successfully.
I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump
The trajectory which I read in VMD has 3008 frames and my ligands
completely disappear after 8 frame (They are not in PBC windows
which I checked in Graphics -> Graphical Representation -> Periodic)
Your choice of trjconv workflow demands that the protein be allowed
to diffuse away. What VMD makes of that is not really of consequence
to discuss here. Perhaps you can design a better trjconv workflow,
as here
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Thank you. I managed to fix it using:
trjconv -f md.trr -o md1000.xtc -skip 4 (1000 frames instead of 4000)
Then accoring to the workflow (PBC) I used:
trjconv -f md1000.xtc -s md.tpr -pbc mol -o mdmol.xtc
trjconv -f mdmol.xtc -s md.tpr -center -o mdCENTER.xtc (Center on a
protein, output - System)
trjconv -f mdCENTER.xtc -s md.tpr -fit rot+trans -o mdFit.xtc (Protein,
output - System)
However, all ligands jump rapidly
around the protein till the time they bind to the protein surface (and
the begining they were randomly placed around the protein) one by one.
At the end when all of them stacked on my protein everything is ok. Will
you suggest something?
Is this unusual? It sounds like the molecules diffuse around until they bind to
the protein. You're centering on the protein and then fitting its translation
and rotation; everything else will be processed relative to those criteria.
-Justin
--
========================================
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
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