[gmx-users] box of simulation

mohammad agha mra_bu at yahoo.com
Tue Aug 14 09:27:14 CEST 2012

Dear Gromacs Users:

When I want to place 12000 solvent  molecule in the box (15*15*15)  it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
             does not match topology (topol.top, 37950)
it means that I should enlarge the box to place all of solvent molecules into that.
But when the system equilibrium with running pr.mdp, box become smaller till 13.9*13.9*13.9!!!
What should I do with this problem?
Is it a problem?!

Thank you very muchin advance.
Best Regards

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