[gmx-users] minimization of particular residue/atom

[Mark Abraham]

That procedure can work. That it works in your case surprises me a little.
:-)

Mark

On Thu, May 2, 2013 at 11:25 AM, gromacs query <gromacsquery at gmail.com>wrote:

> Dear Mark,
>
> I found a simple(est) fix to this problem. Say in my case I was getting
> error inf on atom 4281 ( Maximum force     =            inf on atom 4281)
>
> What  I did: In gro file for atom number 4281 I edited one of its
> coordinate just 0.1nm that is 1 Angs e.g. 6.518 to 6.618 (I did for x, but
> can be y or z). So mdrun was complaining one by one and I edited in all
> three such x coordinates for three atoms. finally I was able to achieve
> convergence.
>
> I believe moving just 0.1 nm minimization will take care of correct
> lengths. May be if its not the correct way; please suggest.
>
> regards,
>
>
> On Thu, May 2, 2013 at 12:50 AM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > On Wed, May 1, 2013 at 4:20 PM, gromacs query <gromacsquery at gmail.com
> > >wrote:
> >
> > > Dear All,
> > >
> > > I am using Charmm gui built membrane (120 x 2). But during
> minimization I
> > > was getting error.
> > >
> > > Potential Energy  =  4.6809051e+19
> > > Maximum force     =            inf on atom 4281
> > > Norm of force     =            inf
> > >
> > >
> > > (inf means? means infinite/NAN)
> > >
> >
> > All the above means your system is
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> >
> > I removed the  full lipid residue having atom number 4281. I was again
> > > getting error representing some other atoms so finally I removed three
> > > lipid residues. Doing this I was able to complete convergence.
> > >
> > > I have two queries:
> > >
> > > 1) As I have removed three residues from Charmm gui membrane, does this
> > > affect final results? Although I will be doing MD for membrane first.
> > >
> >
> > Maybe. We don't know whether the membrane was built wrongly, or you
> > post-processed the coordinate file wrongly, or whether you need all the
> > lipid molecules to achieve the right density, or...
> >
> >
> > > 2) Also is there any way so that particular atoms can be minimized or
> > > ''touched'' ? Here in this case I removed three lipid residues but this
> > > will not be good say in case of proteins. Just as a analogy if this
> > problem
> > > arises  in AMBER (rather I faced such problem many times) I can use
> xleap
> > > and can move atom a little and relax it particularly by selecting it ,
> so
> > > that later if use the edited structure I get convergence properly
> without
> > > error.
> > >
> >
> > You can only do that by moving the coordinates by hand in the coordinate
> > file before you give it to grompp. Your PE above is so large that this is
> > not the right approach to fix the problem. I would guess your periodic
> box
> > is not the one you were intended to use.
> >
> > Mark
> >
> >
> > >
> > > regards,
> > > Jio
> > > --
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