[gmx-users] Energy minimization

[Peter C. Lai]

It depends on what the atom is overlapping with and some conjecture as to 
what might be causing the overlap:

You can always manually move it, either by editing the .gro file directly
or using a tool like VMD to move it or the molecule/fragment it's attached to
with the mouse and then display the new coordinates and the update the .gro 
file.
If it's something like a solvent molecule (water/lipid) and there is nowhere 
to move the molecule, you can try deleting it too (just remmeber to update 
.top file).

On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote:
> When I find overlapping atom, what should I have to do? How is it possible to get solved?
> 
> 
> Would you please help me? 
> 
> 
> 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.
> >
> > 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
> 
> -- 
> ========================================
> 
> 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
> 
> ======================================== 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--