On 1/20/13 7:34 AM, Mehdi Bagherpour wrote:
I use bellow commands but still in some of snapshot trajectories, two
strand of DNA separated from each other in VMD.
trjconv -s md.tpr -f md.xtc -o md.pdb -center
trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -ur compact
trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center -ur compact
trjconv -s md.tpr -f md.xtc -o md.pdb -center -ur compact
None of these involve an index group. As I said, you may have to choose some
custom subset of atoms to serve as a centering group. The -center option places
the geometric center of the chosen group at the center of the box; if there are
two molecules, then the center of this group can still coincide with the center
of the unit cell if both molecules are at opposite sides of the box.
-Justin
On Sun, Jan 20, 2013 at 3:38 AM, Justin Lemkul <[email protected]> wrote:
On 1/19/13 5:21 PM, Mehdi Bagherpour wrote:
hello everybody
I have simulated DNA using CHARMM force field for 50 ns with 2 ps
snapshots
for each step.
when I wanted to convert .xtc trajectory files to .pdb using trjconv,
some
of the snapshots were collaborated.
I have used periodic boundary conditions in this simulations.
To convert, I used bellow command:
trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center
In collaborated .pdb files two strands of DNA separated from each other.
when I used bellow command instead of above command, this collaborated
.pdb
file will be corrected,
but some of the other .pdb files will be ruined as same as
trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol
would you please help me to solve this technical problem?
Use -center, perhaps in conjunction with some custom index group that will
serve as an adequate central group for processing.
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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