vidhya sankar wrote:
Dear justin,
Thank you fro your previous reply
when i run SMD using the same force ( same rate constant and same rate)
in different box having different dimension. will it affect the result
of simulation
I am asking the effect of box dimension on pull in group (keeping
constant rate and rate constant)
I am expecting your valuable reply
Thanks in ADVANCE
Possibly, but your question is too vague to give any real advice. Are you
adjusting all box vectors, or just along the pulling dimension(s)? How far are
you pulling? Does the pulled distance always remain less than 1/2 the box
vector along the pulled dimension(s)? Or are you using the direction_periodic
geometry to circumvent this effect?
-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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