[gmx-users] problem with MD

Dastmalchi dastmalchi.s at tbzmed.ac.ir
Sun Nov 2 13:08:01 CET 2003

Dear Colleagues,

I am trying to do the same procedure on my protein containing a cofactor as described in the GROMACS Tutorial for Drug-Enzyme complex (by John Kerringan). Things were going ok (as far as I can see) until I tried to run MD of my system. i.e., issuing the following command:

mdrun -s xxx.tpr -o xxx.trr -c xxx.gro

It goes few lines and after the following lines it stops and doesn't go further. 

atom1 atom2 angle previous, current, constraint length
6446    6447    38.9    0.1080    0.1080    0.1080
9060    9061    90.0    0.1080    0.1650    0.1080
9840    9841    43.6    0.1080    0.1080    0.1080

The CPU of the computer is almost fully engaged by mdrun program, however it doesn't move further.

I know that it is hard to rectify such problem with such a short description, however, I will appreciate it if you could kindly let me know what is the problem.


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