[gmx-users] Load imbalance and Y size error

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 8 09:16:56 CEST 2009

nikhil damle wrote:
> Hi,
> I tried to run on single node now. Now the error is different saying
> "One of the box vectors has become shorter than twice the cut-off length 
> or box_yy-|box_zy| or box_zz has become smaller than the cut-off"
> This means that my box shrinks during dynamics (this is not constant 
> volume MD) But when Solvent is present in the same system, this does not 
> happen. How should i deal with it then ?

If it's not constant volume then the simulation will change volume. Why 
should your charged proteins want to stay at the original distance from 
each other? It seems they want to collapse onto each other. You need to 
rethink your choice of ensemble.


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