Gaurav Chopra wrote:
/ Hi
/>/
/>/ I get the following error when using mdrun for a protein in
solution. />/ I have checked the structure and everything looks fine
to me. Could />/ you suggested anything else I could do. /
How did you energy minimze your structure? What was the output of
mdrun during energy minization, especially the last line with Fmax,
Epot etc.?
I should look like this:
Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05,
atom= 78754
Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03,
atom= 13032
Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04,
atom= 13032
Jochen
Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And
have you run a minimization before starting the simulation?
hear from you soon
Steffen
-----------------------------------------------------------------------
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
Gaurav
--------------- mdrun log file output ------------------
Better show us the output of your energy minimization. The ouput of your
md only shows that your sctructure has some serious problem...like your
box is too small or whatever...
Jochen
--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
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