Jennifer Williams wrote:
Hello,
I am trying to find a way around a visualisation problem I am having in
VMD. Some of my molecules go over periodic boundary conditions meaning
that bonds sometimes appear missing when looking at movies (I am trying
to fix this using wrap, unwrap and join in VMD but as yet no luck).
I was wondering if there is a way in gromacs to multiply the number of
unit cells shown in a trajectory. i.e instead of a 1x1x1 I want the new
unit cell to be 2x2x2. This would mean the section of the structure I
want to zoom in doesn't go over the pbc.
For the confout.gro file I have done this using
genconf -nbox 2 2 2 -f confout.gro -o confbig.out
and this enables me to at least see a static image where all bonds are
present.
but in order to view a movie, I need to carry out something similar on
the traj.xtc file. I have seen that with trjconv there is the option
-box Size for new cubic box
but my unit cell is not cubic, it is a parallelepiped. The cell
dimensions are :
4.64210 3.77847 1.89596 0.00000 0.00000 -2.18150 0.00000
0.00000 0.00000
I tried using this anyway with the following command:
trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc
but the resulting .xtc file wouldn't load into VMD so I assume that the
.xtc file and the .gro file didn't match.
Correcting periodicity should alleviate some of the problems. Using trjconv
-pbc mol (or -pbc nojump) is typically the best first step.
-Justin
Any ideas?,
Thanks
Jenny
--
========================================
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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