Shyno Mathew wrote:
Hey Justin,
thanks for your reply.
For gen_vel, the manual says "Generate velocities in grompp according to
a Maxwell distribution at temperature gen_temp [K], with random seed
gen_seed. This is only meaningful with integrator
md"
Since the integrator I am using is sd, I put 'gen_vel no'
Ah, I guess I missed that before.
Yes you are correct, this is equilibration.
From what you are saying, even with sd as the integrator, I guess, I
should put
gen_vel yes
gen_temp 310 ; i want to do the simulation at 310K
As I said before, you've changed too many variables simultaneously (not very
scientific ;) to pinpoint exactly what the problem is. Systematic changes, as
prescribed by your force field and chosen algorithms, are the only suitable way
to run a simulation. Right now, it's a pure guess as to what went wrong.
-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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