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 this- 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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