I concur with what Mark suggested about in vacuo EM. I would also point out the
following problem(s):
and the md.mdp:
Here you call for 300 K as the reference temperature and the temperature at
which you've equilibrated:
tc-grps = Protein Non-Protein
tau-t = 0.1 0.1
ref-t = 300 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 290K - do not get velocity from gro file.
And here you're destroying the previous equilibration by re-generating
velocities and simultaneously generating velocities for the wrong temperature,
which may or may not induce instability into the system.
gen_vel = yes
gen_temp = 290
gen-seed = -1
-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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