On 1/17/18 9:40 AM, Rose wrote:
You mean if -pbc could make molecule whole,everything is ok, but if not it
means the molecule was broken from first, yes?
mdrun writes "broken" coordinates because the physics does not depend on
our visualization convenience. Most programs account for PBC. Some
don't. It is generally a safe practice to just make molecules whole as
your first step in trjconv and avoid any ambiguity.
-Justin
Sent from my iPhone
On Jan 17, 2018, at 16:19, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/17/18 5:51 AM, Vidya R wrote:
Hi Justin,
I got the same result as you said.
What confused me was, when I viewed movie.pdb file generated by the
following command,
gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 10000.0 -n
index.ndx -o movie.pdb
two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be). They are far away from molecules (their
bonds were broken)
Is it a pbc problem?
Because, when I used
gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc
and created a .pdb file with newtraj.xtc, the whole molecule was intact.
Making molecules whole should always be the first step. If you try to remove jumps with
"broken" molecules, what you visualize will be garbage. A separate issue is
with respect to the analysis programs - many are PBC-aware and can handle the original
trajectory without manipulation.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
