[gmx-users] Re: Energy Drift in Gromacs 4.0

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 12 03:59:11 CET 2009

Ilya Chorny wrote:
> If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE 
> simulation they should counter balance. I am leaking K.E. somewhere. I 
> reran with a relaxed P.E(t) and saw the same behavior.  This is 
> happening both at 2 and 4 fs so its not a time step issue. Any thoughts? 
>  I thought it might be COM removal so I turned it off to no avail. 

"going down" is seriously unhelpful. I told you you needed to 
equilibrate before measuring such things. If you want people to take 
your problem seriously, you'll need to announce that you have 
equilibrated and for how long and in what ensembles, etc. If you're 
having a problem, you need to demonstrate what areas you feel are not 
causing it. We're not your family doctor who will ask a pile of 
questions to find out the problem :-)


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