[gmx-users] box size changed

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 1 02:15:02 CET 2007

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?


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