Justin A. Lemkul wrote:
Sanku M wrote:
Hi Justin,
I first performed two minimization using steep and l-bfgs as the
method on the solvated system for each lambda. Then I ran a 500ps NVT
simulation on minimized system ( for each lambda) where essentially
same .mdp file was used except the following change:
gen-vel = yes
gen-temp = 280
gen-seed = -1
So, essentially, I heated the minimized system up from 280 K with
ref_t 300K using sd integrator. But, here also I found the average
temperature goes to 303 K( instead of 300 K) .
Unless you did simulated annealing in between, you didn't heat the
system, you suddenly jolted the temperature, which is probably not
stable. Maybe the integrator/Langevin thermostat does not react well to
these conditions. Equilibrate under the conditions you wish to collect
data. Your data collection uses NPT, so running NVT at a different
temperature and suddenly changing the temperature and introducing
pressure coupling is not an appropriate procedure. If nothing else, your
data will be unreliable, even if your temperature was correct.
Sorry, misread the previous .mdp settings. You're still using NVT, but the
point about the temperature is still valid here.
-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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