Sanku M wrote:
Hi,
I have a molecule consisting of 4 sites which have fixed relative
positions interacting only through LJ and coulomb interaction. I was
wondering how can I do MD simulation in GROMACS keeping the geometry
unchanged . Is just putting constraints along all the possible
distances and using LINCS good enough for maintaining the geometry ? Or
I suspect it is, and I would imagine it would be easy enough to determine that
with a short test.
, Does one need to also make sure the angles are also unchanged but I am
not sure how to do that ? I was wondering what will be an optimum ways
You can also set "constraints = all-angles" in the .mdp file.
of dealing with such a 4-site system. I guess, Settle can not be used
for such a 4-site system.
Nope, SETTLE shouldn't be relevant here.
-Justin
Thanks
Sanku
--
========================================
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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