Please change the subject line to the relevant topic and do not paste the entire
digest. I guess the archive is already somewhat hopeless, but let's not make it
worse :)
Saba Ferdous wrote:
Dear Justin,
I have set 1.5 dodecahedron. i centered the complex in box.
complex.gro, complexsol.gro and complex_sol_ions.gro seems inside in
box. I m using VMD for visualization. i have rotated it in 3D
while when after EM step, i visualize em.gro then half complex seems
outside the box. is there any way to center em.gro after energy
minimization?
Again, this is just a matter of visualization. There is nothing wrong and
nothing needed to fix. You can rewrap the periodic cell with
trjconv -pbc mol -ur compact
if you find you want more convenient visualization.
-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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