On 12/04/2010 5:01 AM, Sanku M wrote:
Hi,
I am having a problem with running a NVE ( micro-canonical) ensemble
using a system of 128 Martini DPPC lipids. I started the simulation with
a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT
ensemble ( using berendsen temperature coupling at 325 K( separate
coupling for lipid and water) and pressure coupling at 1 atm for 500 ns).
But, when I started running the NVE simulation by switching off pressure
coupling and temperature coupling, the temperature started going down
from 325 to almost 2 K very quickly which looks like very unphysical.
However, total energy remains conserved . But the temperature is
becoming a concern as it is going down to a 0 K. I am not sure whether I
am doing some mistake in the mdp parameter. Any help will be appreciated.
I don't know anything about running Martini simulations but I could see
that the following are not consistent with running a pre-equilibrated
system:
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 325
gen_seed = 473529
You want to keep the old velocities, not make new ones. See some
tutorial material or the webpage about run continuations for
instructions here.
I don't know if this is the cause of your problem, however.
Mark
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