Qian Wang wrote:
Hi,
I use Gromacs4.0.5 to run a 20 ns npt simulation in periodic boundary
box. At first I put peptide in the center of the box, then I write
comm_mode = linear in *mdp file. However, the peptide still moves out of
the box and go through to the other side of the box. Is there any method
that can solve this problem?
What you're seeing is entirely normal:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Another question is that after the peptide accross the box like I said
above, I think if I want to use g_dist I should use "trjconv -nojump"
first. Then if I use the umbrella sampling method and use g_wham -it
tpr.dat -ix pullx.dat to analyze the data. Do I need to do any other
steps before I use the g_wham command?
Most Gromacs tools deal with PBC intrinsically, so g_dist may not need this
correction to work properly. Run an analysis with and without PBC correction to
convince yourself.
Lots of periodic jumps may confuse g_wham, but I don't know offhand. It is
probably preferable to avoid such jumps during mdrun to avoid bad interpretation
of PBC, but without a lot more information about how you set up your system,
there's not much more to say. There is a tutorial linked from the Gromacs site
that explains a reasonable method for preparing a pulling system.
-Justin
Thanks a lot.
Best,
Qian
--
========================================
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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