Vitaly Chaban wrote:
For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct
to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Setting a box size and using "pbc = xyz" precludes the use of infinite cutoffs,
which should be the most rigorously correct way to treat this type of system.
With PBC, there are long-range effects that should be avoided.
Nilesh: visualize your system, using VMD or ngmx. The behavior of your
molecular cluster during the first ps will provide an answer. Are you
sure that your topology is healthy?
I agree with this. The system should be going absolutely haywire :)
-Justin
--
========================================
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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