On 1/16/13 10:09 AM, Kieu Thu Nguyen wrote:
Dear All,
I want to merge two or many boxes with the same size into one new box. The
size of new box is not a multiples of old box size. And the molecules that
overlap have to be removed. In Gromacs, are there any tool for my problem ?
See the logic of constructing heterogeneous systems here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
You can position one component anywhere in a unit cell with editconf -center,
and potentially fill the other half with a solvent using genbox -cs, which will
remove overlapping molecules, but any system more complex than stacking a few
boxes in the same dimension will not be very easy. With the editconf -center
method, one could conceivably place any number of boxes anywhere in the unit
cell, but there is no automatic removal of overlapping atoms.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
