simon sham wrote:
Hi,
I) I have been trying to figure out where is the source of the following
warning message coming from:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
from the correct mass and radius of the atom type.
It would be useful to know what program is issuing this statement, what your
command was, what you're doing, etc. Presumably, whatever program it is needs
van der Waals radii and is going to make a guess as to what they should be based
on atom names rather than types. Using a run input file usually alleviates this
issue.
2). I used ngmx to inspect the trajectory of a 20ns MD run, and I
noticed that the protein is moving around quite a bit in different
directions. Is it normal?
All molecules diffuse. Otherwise, see FAQ #11, which is a question that gets
asked weekly, if not more frequently.
http://www.gromacs.org/Documentation/FAQs
-Justin
Thanks for your insight.
Simon
--
========================================
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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