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Hi
I used the initial minimization run using grompp and mdrun using
steepest descent for 400 steps and 0.002 ps as the step size. The
constraints are all-atom.
The following is the output from the log file that was generated after
the md.
Any suggestions?
Thanks
Was the system already completely munimized, i.e. has it reached
convergence? 400 steps seems a bit small to me. I usually had problems
with the constraints when the system had some kind of "point of frition"
where a bad contact was still existing. Did you check which where the
atoms mentioned by the lincs warning or if there were bad angles or
contacts in the starting structure?
--
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
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