[gmx-users] problem during energy minimisation using cg integrater
sharmanitu35 at gmail.com
Mon Jul 6 06:59:54 CEST 2009
Dear all ,
I am trying to energy minimisation of one protein
molecule but during the grompp mdrun I am facing error again and again like
t = -0.000 ps: Water molecule starting at atom 35705 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step-1b.pdb to ./#step-1b.pdb.2#
Back Off! I just backed up step-1c.pdb to ./#step-1c.pdb.2#
Wrote pdb files with previous and current coordinates
I am using conjugate gradient intigrater to minimise this protein after
doing 100 steps steepest descent minimisation.
my em.mdp file like this-
cpp = /usr/bin/cpp
define = -DPOSRE_PROTEIN
constraints = none
integrator = cg
dt = 0.0001
nsteps = 1500
; Energy minimizing stuff
emtol = 100
emstep = 0.001
nstcgsteep = 1000
nstcomm = 1
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
coulombtype = PME
Tcoupl = no
Pcoupl = no
gen_vel = no
comm-mode = Linear
pbc = XYZ
If anyone have idea regarding this please suggest me to solve this problem
for this I will be really thankful to him/her.
thanks a lot.
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