[gmx-users] stochastic dynamics parameters

Fan Hao f.Hao at chem.rug.nl
Tue Jul 15 04:21:02 CEST 2003

Hi, All:
	I did stochastic dynamics of protein GB1 with
G9643a1 FF and published gmx3.0.5. When I set the
epsilon_r to be 1, the Coulomb (SR) energy of the
starting conformation which was optimised by EM
is around -9000 kj/mol. This value is much higher 
than what I get from Gromos package with every setting
the same. I am not sure whether I set the parameters
correctly in my mdp so I put them here. Any hints
will be sincerely appreciated!

integrator = sd
nstcomm = 1
nstlist = 0
ns_type = simple
pbc   = no
rlist = 0
coulombtype = Cut-off
rcoulomb    = 0
epsilon_r   = 1
vdwtype     = Cut-off
rvdw        = 0

Best regards

Yours sincerely

Hao Fan :-)

Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands

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