On 14/08/2012 5:27 PM, mohammad agha wrote:
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
What's "it"? genbox? grompp? You can't be helped effectively if you
don't provide your command lines that produce output, and/or a
description of what's already in your system.
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.
Nobody can tell from the information given.
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?
You've asked for a constant-pressure ensemble, so the volume will not be
constant. So it can change. How it changes depends what's in it. What
happens if you magically take a bunch of air out of an inflated balloon?
Mark
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