[gmx-users] box of simulation
Mark.Abraham at anu.edu.au
Tue Aug 14 10:29:10 CEST 2012
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?
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