arun kumar wrote:
hi justin, I accept with u that simulation will not complete in 3ns, but
as iam trying simulation at 400k for the first time i just kept it for
3ns to see how it will be.
and for checking conformational changes i saved the structures for each
100ps from the trajectory (is it a correct procedure for that.....?)
Maybe, maybe not, it's hard to guess. The magnitude of the conformational
change will dictate how long the simulation has to be and the correlation
between configurations (i.e. how slow the motions occur) will dictate how
frequently you should sample to get statistically independent configurations.
and is it possible to give explanation for the parameters and forcefield
that we need to fallow for higher temperature simulations......?
Look to the literature for precedent. REMD is done routinely in the 400K range.
You may need a shorter-than-usual timestep (i.e. 1 fs, even with constraints)
and NPT is unlikely to remain stable since the water density will decrease over
time.
Please remember to delete the text of the digest before sending.
-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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