[gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

HAO JIANG hj.public at gmail.com
Mon Nov 30 18:01:30 CET 2009


I got a problem with the output structure files (gro/trr/xtc) generated by the energy minimization with GROMACS 4. That is, when I used the generated structure as the input for further minimizations or MD simulations, I got very large potential energy and forces at step 0, as if the structure had not been optimized at all. On the other hand, there is no problem when the input structure is taken from a previous MD run, and I got the expected potential at step 0. There is no problem, too, if I use GROMACS 3 to do the minimization. 

Any help is greatly appreciated!

Hao Jiang
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