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