[gmx-users] Normal Mode Analysis

[James Starlight]

Justin,


I've forced with the problem that I could not prorerly minimized my system
in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot
value lower than +3.00 with that parametries ( I've used KALP peptide as a
test input )

; Parameters describing what to do, when to stop and what to save
integrator    = steep
emtol        = 1      ; Stop minimization when the maximum force < 1.0
kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps        = 5000000          ; Maximum number of (minimization) steps to
perform



; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 1        ; Frequency to update the neighbor list and long
range forces
ns_type        = grid        ; Method to determine neighbor list (simple,
grid)
rlist        = 1.2        ; Cut-off for making neighbor list (short range
forces)
coulombtype    = Shift
rcoulomb        = 1.0
rcoulomb_switch    = 0.0
vdwtype         = Shift
rvdw        = 1.0
rvdw_switch     = 0.0

Than I've tried to futher minimized this structure via  l-bfgs algorithm by

integrator    = l-bfgs
dt                  =  0.01
emtol        = 0.001     ;
emstep      = 0.1      ; Energy step size
nsteps        = 50000000          ; Maximum number of (minimization) steps
to perform

but Epot was still big.

What I've done wrong ?
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