Steven Neumann wrote:
On Mon, Jan 30, 2012 at 1:46 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Steven Neumann wrote:
On Mon, Jan 30, 2012 at 12:16 PM, Mark Abraham
<[email protected] <mailto:[email protected]>
<mailto:[email protected].__au
<mailto:[email protected]>>> 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
<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
Sorry, I did not clarify it properly. What is unusual is that
my ligands (until they bind) jump to its periodic images. It is a speed
light diffusion :) Any suggestions?
Nope. As I said, you fitted everything on the protein (which is sensible).
Everything else is manipulated accordingly. Perhaps it's a bit inconvenient to
watch, but there's no real way to avoid periodic jumps of every molecule
simultaneously, you need a reference position, which for you is the protein.
-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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