[gmx-users] simulation a box of water

Saeed Nasiri s.t.nasiri at gmail.com
Sat Apr 2 11:22:36 CEST 2016

thanks again.

I did the recommended option in the grompp command , but there a problem
with minimization step. the error is
"Water molecule starting at atom x can not be settled".
I checked the previous emails and I did a few things but I can't solve it.
In the previous emails, it was recommended to reduce the timestep and I
used (0.1, 0.01, 0.001, 0.0001) steps.
Also I checked the produced pdb files after that the programs stopped and I
see that some of the water molecules stretch out along the box.
I don't know how to fix this problem?

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