[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?

Would you please help me? 


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.
> Any suggestion please? I don't know how to solve this problem. Please help me.

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



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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