[gmx-users] mdrun

[Justin A. Lemkul]

leila karami wrote:
> dear chris
>  
> I did EM :
>  
> Steepest Descents did not converge to Fmax < 2000 in 101 steps.
> Potential Energy  = -3.2421097e+05
> Maximum force     =  1.4766100e+04 on atom 1441
> Norm of force     =  2.5146213e+02
>  
> I am sure that  constraints=none during EM.
>  
> how do I increase  the LINCS/SHAKE iterations to the appropriate number?
>  this is my em.mdp file

The better approach is to run more than 100 steps of EM.  Your force is still 
unacceptably high, which is likely what is causing the crash you see later.

-Justin

>  
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> nsteps              =  100
> ;
> ;       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
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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