[gmx-users] box of simulation

Mark Abraham 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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