Re: [gmx-users] mdrun error

[Kester Wong]

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 <lovikamoud...@gmail.com>
받는사람 : <gmx-us...@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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