[gmx-users] MdRun Crash
samikbhat at yahoo.co.in
Mon Jul 6 13:13:08 CEST 2009
I am running a simulation of a membrane protein in DPPC bilayer. ii have completed upto genion step. But when i am going to minimize the energy of the system the mdrun crashes showing
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -9.8290938e+21
Maximum force = 6.7779973e+24 on atom 5591
Norm of force = 2.4384918e+22
i can understand the problem lies in the mdp file used, i.e. in the Epot and Fmax. i have rerun the step using different values but with same result.please suggest me how to overcome the constraints problem. thanking you in advance. mdp file is here
integrator = steep
emstep = 0.001
emtol = 1000
nsteps = 5000
nstlist = 1
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
pbc = xyz
Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users