[gmx-users] mdrun error

[Mark Abraham]

Hi,

Use a visualization program and see what you learn...

Mark


On Mon, Aug 25, 2014 at 8:26 AM, Lovika Moudgil <lovikamoudgil at gmail.com>
wrote:

> I am  trying to have a system of  GNPs with aminoacid and stabilizer i.e
> Sodium Citrate ...and this hydrogen is of Sodium Citrate .....  moving
> molecule is not working for me!!!
>
> Regards
> Lovika
>
>
> On Mon, Aug 25, 2014 at 10:52 AM, Kester Wong <Kester2014 at ibs.re.kr>
> wrote:
>
> > If the H-atom is constituent of a molecule (e.g. H2O), then you could
> also
> > try moving the molecule coordinates and see how it goes.
> >
> > I had a similar issue, but moving the molecule by an angstrom worked in
> my
> > case. Good luck!
> >
> >
> >
> > Regards,
> >
> > Kester
> >
> >
> >
> > --------- 원본 메일 ---------
> >
> > *보낸사람* : Lovika Moudgil <lovikamoudgil at gmail.com>
> > *받는사람* : <gmx-users at gromacs.org>
> > *받은날짜* : 2014년 8월 25일(월) 13:52:49
> > *제목* : Re: [gmx-users] mdrun error
> >
> > Thanks for reply Justin and Kester...Ya my geometry is getting distorted
> > and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the
> > error is same!!!!
> >
> >
> > Regards
> > Lovika
> >
> >
> > On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong  wrote:
> >
> > > Dear Lovika,
> > >
> > >
> > > Have you looked into atom 19 specifically? Perhaps, changing the
> > > coordinate of atom 19  manually, and let it do another minimisation run
> > > would solve the issue?
> > >
> > >
> > >
> > > Regards,
> > >
> > > Kester
> > >
> > >
> > > --------- 원본 메일 ---------
> > >
> > > *보낸사람* : Lovika Moudgil
> > > *받는사람* :
> > > *받은날짜* : 2014년 8월 24일(일) 18:28:06
> > > *제목* : [gmx-users] mdrun error
> > >
> > > Hi everyone ,
> > >
> > > Need some help .I have got an error in my mdrun . Upto grompp every
> thing
> > > was fine but when I give command for mdrun ,It stops with this ...
> > > Steepest Descents:
> > >    Tolerance (Fmax)   =  1.00000e+03
> > >    Number of steps    =        10000
> > > Step=   14, Dmax= 1.2e-06 nm, Epot=  2.08534e+18 Fmax=         inf,
> atom= 19
> > > Energy minimization has stopped, but the forces have not converged to
> the
> > > requested precision Fmax < 1000 (which may not be possible for your
> system).
> > > It stopped because the algorithm tried to make a new step whose size
> was too
> > > small, or there was no change in the energy since last step. Either
> way, we
> > > regard the minimization as converged to within the available machine
> > > precision, given your starting configuration and EM parameters.
> > >
> > > Double precision normally gives you higher accuracy, but this is often
> not
> > > needed for preparing to run molecular dynamics.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints altogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > >
> > > Steepest Descents converged to machine precision in 15 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  =  2.0853354e+18
> > > Maximum force     =            inf on atom 19
> > > Norm of force     =  1.7429674e+18
> > >
> > > constraints are all ready none ...Please help me what should I do to
> solve
> > > this .
> > > Thanks and Regards
> > > Lovika
> > > --
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