[gmx-users] Energy minimization

Wed Dec 19 06:28:44 CET 2012

Read through the log file to find out what atoms are causing the system to 
crash. I also prefer running mdrun -v and capturing that too, since it
provides similar log data but does not output the energy tables.

You also did not specify what the final maximum forces were in the system
after the last round of minimization or what atom had the highest force
at the end of the EM.

If you did anything weird with the protein, you may have to go through the 
entire structure sidechain by sidechain to make sure that there are no weird
connectivities (Once I had a peptide bond from a coil going straight through 
the plane of a benzene ring in a far-away residue, and the simulation would 
always crash because the forces of the covalent bonds in the ring would blow
up as it clashed with the forces calculated for the peptide bond and this was 
not noticed during minimization). 

On 2012-12-17 03:04:47AM -0800, Shima Arasteh wrote:
> 
> 
> 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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