[gmx-users] Energy minimization

[Shima Arasteh]

Dears,
I changed the coordinates of overlapping atoms and got a normal potential energy. Then when I go to the next step ( NVT equilibrium ), it doesn't run and I just get some pdb files. How is it possible to find the problem?

It might be clashes in the system but How can I find the overlapping atoms and the reason of clashe among a vast number of atoms?


Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, December 16, 2012 11:18 AM
Subject: Re: [gmx-users] Energy minimization

Probably remove the overlapping lipid then. Once you run MD it will repack.

On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote:
> 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?
> 
> Thanks.
> 
> 
>  
> Sincerely,
> Shima
> 
> 
> ----- 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>
> Cc: 
> 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 
> 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
> > 
> > ======================================== 
> > -- 
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