On 4/19/13 4:37 PM, Brad Van Oosten wrote:
Ahh, yes perhaps i was unclear. The output file also has the same number of
steps.
Checking file md50_centered.xtc
Reading frame 0 time 0.000
# Atoms 27392
Precision 0.001 (nm)
Last frame 50000 time 100000.000
Item #frames Timestep (ps)
Step 50001 2
Time 50001 2
Lambda 0
Coords 50001 2
Velocities 0
Forces 0
Box 50001 2
The simulation is of a pure lipid bilayer, so the result of the centering
option is that 99.9% of output frames have the lipid tales centered in the
box while the 0.1% of frames seem not to be centered with the water at the
center of the box.
This is not an issue of skipping frames at all, then. It is an issue of your
perception of "center," one that has been discussed many times on this list.
This often happens with systems of lipids, multimeric proteins, or
receptor-ligand complexes. The "center" of a system is the geometric center, so
two molecules together at the visual center of the box and two molecules on
opposite "sides" of the box are both considered "centered" since the geometric
center of the group coincides with the geometric center of the box. Several
iterations of trjconv (including -pbc or -fit options, in separate steps) may be
necessary to achieve the desired outcome.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
-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
