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

Luca De Gaetani degaetani at dcci.unipi.it
Thu Mar 12 10:55:47 CET 2009

Even if a system is not well equilibrated (but not so far from 
equilibrium) ,energy should be conserved in NVE ensemble.
Try to lower the nstlist from 10 to 1 i.e. renew every time the 
neighbourlist. In systems I have studied, that is the key that improve 
much more energy conservation. It works even without switching of VdW 

Luca Dre Gaetani
> Message: 1
> Date: Thu, 12 Mar 2009 13:59:11 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: Energy Drift in Gromacs 4.0
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49B87A7F.30807 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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 :-)
> Mark

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