[gmx-users] box size changed

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 1 12:06:42 CET 2007


My guess is that you have pressure coupling on. Now, what is the
characteristic of vacuum? What will happen if you have a balloon
filled with vacuum (and one small red car of almost negligible size)
and you couple it to a reference pressure (keep it out in the

In the other case, you may see diffusion over the periodic boundaries,
or the system is relaxing due to some cause, but it's hard to guess
since you don't give any information. Now, take a look under the hood
of your car (the .mdp file) and see what direction it is said to go,
paying explicit attention to pressure coupling and temperature. Also,
read a bit about periodic boundary conditions, doing simulations in
solvent and doing simulations in vacuum.



On 3/1/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Nancy Deng wrote:
> > Hi Mark,
> >
> > Thanks for the quick response and the funny story :)
> >
> > I indeed want to collect the possible comformation of a certain small
> > molecule (a little car made of 35 atoms around 15 A in length) by MD.
> > Since obvious to my understanding that in vacume or in water
> > environment, the small molecule could behave quite different (i really
> > want to see this happens :). So, my goal is to compare the difference of
> > the two MD trajectories ( for example 5 ns or even longer) of the small
> > molecule by Gromacs. But i am stuck even at the very beginning which i
> > could never reach either New York or Detroit :(
> >
> > In the case of no-water simulation, the box without water was generated
> > by "editconf" but not followed by "genbox" to avoid water filling in.
> > The other box was consequently generated by "genbox" to contain 370 SPC
> > water molecules. During the equilibration stage, the water particles
> > seems prefer to roam away  from the originally centered small molecule,
> > which i guess the reason to increase the overall size of the box...
> >
> > Not sure whether this provides some useful input to help me out of the
> > trouble :)
> We need to know the kind of simulation you're attempting (ensemble,
> etc.), the size box you're using and its density, your equilibration
> regime, whether you got any warnings from grompp, and probably other
> stuff I can't think of now, in order to tell where you're breaking things.
> Have you tried the tutorial material?
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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