[gmx-users] problem during energy minimisation using cg integrater

nitu sharma 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
Segmentation fault

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.

nitu sharma
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