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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Nov 30 18:37:09 CET 2009

Ni Hao,

You don't give too much information here. What exactly are you doing?
What are the commands? What's the difference between the first and the
second pass of EM? One thing to check is whether the output/input file
has a correct box definition.



2009/11/30 HAO JIANG <hj.public at gmail.com>:
> Hi,
> 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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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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