[gmx-users] Both Steepest and Conjugate didn't converge

[Pradip Kumar Biswas]

Hi Prettina,

I saw the reply of Tsjerk but I want to add that if we use 'simple' 
neighbor search
(ns_type = simple) instead of 'grid', I always get pretty good lower 
energy for e.m.
And once we use ns-type=grid, most of the time we encounter the message
you got. Could you try your energy minimization with ns_type=simple?

pradip.

On Feb 8, 2006, at 12:46 PM, Prettina Anto_Louis wrote:

> Hello gromacs users,
>
>
>            Greetings!
>
>
>                 I am working with a drug-enzyme complex. For my 
> complex, I am facing the problem in the energy minimisation step with 
> both steepest followed by  conjugate . Both of these integrators, 
> didn't converge with the given number of steps. I did the energy 
> minimisation using steepest with the following parameters in the 
> em.mdp file:
>
> ==========================em.mdp(steep)=============
>
> cpp                 =  /lib/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> nsteps              =  1000
>
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.01
>
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
>
> ================================================
>
>   I got the follwing result:
>
>
> Stepsize too small (5.71705e-07 nm)Converged to machine precision,
> but not to the requested precision (2000)
>
> Steepest Descents did not converge in 442 steps
>   Potential Energy  = -7.01019e+05
> Maximum force:  9.58302e+03
>
> ============================================
>
>              So, I again performed the energy minimisation using the 
> conjugate gradient with the following parameters after the steepest:
>
> ============em.mdp(cg)=========
> cpp                 =  /lib/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  cg
> nsteps              =  1000
> nstcgsteep          =  1000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000
> emstep              =  0.01
>
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> Pcoupl              =  no
> gen_vel             =  no
> rvdw                =  1.0
> Tcoupl              =  no
>
> =======================
>
>
>       I got the following output for my CG minimisation:
>
>
> Negative number for sqrt encountered (-75353886948327424.000000)
> Terminating minimization
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.trr to ./#em.trr.1#
>
> Conjugate Gradients did not converge in 927 steps
>   Potential Energy  = -7.80361e+05
> Maximum force:  1.08202e+04
>
> =============
>
>
>            Please let me know, what is the problem with the energy 
> minimisation. Am I going wrong with any of the parameters in the 
> em.mdp file? Please guide me. Should i proceed with my molecular 
> dynamics with this minimised complex coordinates, or should i further 
> minimize the same? Please guide me.
>
> Thanks in advance!
>
>
>
>         "praise the lord!"
>
>
> With prayers,
> prettina
>
>
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