# [gmx-users] Energy minimization

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Dec 16 05:58:59 CET 2012

```When I find overlapping atom, what should I have to do? How is it possible to get solved?

Sincerely,
Shima

________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, September 29, 2012 3:01 PM
Subject: Re: [gmx-users] Energy minimization

On 9/29/12 3:19 AM, Shima Arasteh wrote:
>
> Dear all,
>
> My system contains lipids, protein and water.
> I want to energy minimize it, so ran grompp:
>
>
> # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
>
> and then:
> # mdrun -v -deffnm em
>
>
> The output is:
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Step=   14, Dmax= 1.2e-06 nm, Epot=  2.30004e+17 Fmax=         inf, atom= 518
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.3#
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  2.3000388e+17
> Maximum force     =            inf on atom 518
> Norm of force     =            inf
>
> It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added "constraints=none" to mdp file, But it doesn't make different.
>
>

Atom 518 is overlapping with something nearby.  You will have to visualize the
system to identify the source of the problem.

-Justin

--
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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