Kavyashree M wrote:
Hello,
The set pressure should reflect whatever system you are trying to model.
This statement is not very clear to me.. But when the mdout.mdp file
after grompp
during energy minimization is examined it says -
gen-vel = no
gen-temp = 300
gen-seed = 173529
Even though I have not assigned any velocities in em.mdp file. Thats the
reason why got this doubt about temperature during energy minimization.
I don't see the connection to my comment about pressure, but I'll address this
anyway. There is no temperature during EM. Hence with "gen-vel = no" then no
velocities are generated. The settings for gen-temp and gen-seed are defaults
that are assigned when none are provided in the input .mdp file.
I seem to recall that a pressure term is written during EM, but it is largely
meaningless.
-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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