yuanyuan wang wrote:
dear all,
I am doing a simulation that have many chains in a box , and I
can find a center for them after serval tries.
I use almost every option of trjconv,-pbc
mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger
box, and -boxcenter, -fit ..
still some chain cannot convert into box. them jump from one
box to another ,
is there any ways that they not jump to another box?
thanks a lot.
Use a custom index group to center on some subset of atoms that you want to be
centered in the system. If you try to just center on, for example, "Protein,"
the geometric center may lie in the middle of the unit cell but the chains are
split across periodic boundaries.
-Justin
yuanyuan
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
