On 6/15/12 8:47 AM, tarak karmakar wrote:
Dear All,
I am little unaware of choosing the shape and length of box while
simulating protein in water. I saw in one of the GROMACS tutorials [
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water] in which
they have kept the protein at the center of the box and the distance from any
atom of the protein to the wall of the box as 1.2 nm. [ r_cut off = 0.8 nm ] . I
got the reason for the selection of box length but_*still not clear about the
shape of the box.
*What is the relation between the shape of the box and the computational cost?*
You can save a lot of computational time using a suitable box shape. For a
globular protein like the one in the tutorial, a cubic box is far less efficient
than a rhombic dodecahedron or truncated octahedron. The choice of box shape
should be dictated by the inherent symmetry of the system. For membranes, a
rectangular or cubic box is appropriate. For proteins, it's usually a waste.
These topics are discussed in the manual, section 3.2.
-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
