[gmx-users] Energy minimization
shima_arasteh2001 at yahoo.com
Sun Dec 16 06:19:49 CET 2012
Thanks for your kind reply.
My system is composed of protein packed by lipids. The atoms overlapping, are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not?
Any other suggestion?
----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, December 16, 2012 8:44 AM
Subject: Re: [gmx-users] Energy minimization
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
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
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?
> 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
> gmx-users mailing list gmx-users at gromacs.org
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