[gmx-users] mdrun error

[Lovika Moudgil]

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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