[gmx-users] temperature too low

[w.j.schravendijk at students.pharm.uu.nl]

Dear Gromacs users,

During a 100 ps run of a short polypeptide in a large box of water, the
temperature of the system remains around 200 K, while it is coupled to
300 K. In a previous 100 ps run of the same system coupled at 600 K,
temperature resided around 400 K.

My em is a simple steepest descent, the conditions of my run are given
below. Could it be that the system is too structured? I guess I could then
use a simulated annealing from 600 K to 300 K before the run. But what
wonders me is that that shouldn't be necessary, should it?

Greetings, Pim

coulombtype              = Generalized-Reaction-Field
epsilon_r                = 54 ; als in artikel walser 2001
rcoulomb                 = 1.4
rvdw                     = 1.0
tcoupl                   = Berendsen
tc-grps                  = Protein      SOL
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Berendsen
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
;
; -- VELOCITY GENERATION --
;
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
;
; -- BONDS --
;
constraints              = all-bonds