[gmx-users] Re: Final state not reached in pulling simulation

Neeru Sharma neeru.bioinfo at gmail.com
Fri Jul 13 08:09:10 CEST 2012

Dear Thomas,

Thanks for ur reply. I have visualized my trajectory and found no water
molecule in between. Moreover, there are no residues in between the
"Residue" and GTP molecule too. I feel I have already applied a large force
for the pulling. Still I will consider you suggestion.
One query regarding your suggestion. It one happens to find a water molecule
in between the pulling groups, will removal of that water be a solution,
because during the course of simulation it may happen that some other
molecule again come between? 

Thanks anyways for you reply and suggestions.


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