[gmx-users] Re: Potential energy from a previous configuration mismatch

Justin Lemkul jalemkul at vt.edu
Fri Nov 30 13:26:56 CET 2012

On 11/30/12 4:45 AM, escajarro wrote:
> Thanks for the tip about nstlist, I will make good use of it.
> I also tried the NPT and the NVT ensembles with different temperatures and
> pressures, and I always had blow-up and large energies. Now I tried
> decreasing the time step up to 10 times, but still have blow-up problem and
> the potential energy at the start of the MD is 1E10 times larger that after
> minimization. Most often the contraints give problems, but I have read that
> it is normal and it makes sense. Just in case, I tried different lincs
> parameters, and also shake instead, but always with the same result.
> Is there any other thing I can check?

It's strange that you're getting constraint problems when your .mdp file 
specifies no constraints.  You also have no "bond" energy term in the .log file, 
so it suggests that somehow constraints are actually being used.  Are they 
explicitly defined in the topology?  Is your geometry sensible after EM?  The 
only thing I can really think of is that the minimization without constraints 
led to some kind of distorted geometry that, upon initiation of any dynamics, 
simply fails.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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