[gmx-users] EM & MD

[Justin Lemkul]

On 10/9/12 9:45 AM, Ali Alizadeh wrote:
> Dear All users
>
> I ran energy minimization and mdrun for my system with
>
> EM was a good run :
>
> Run parameters
>             integrator	= steep	
>             dt                  = 0.002
>             nsteps            = 50000
>             emtol             =100
>
> MD was not a good run :
>             integrator	= steep	

This is not MD, you're running energy minimization again.

>             dt                  = 0.002
>             nsteps            = 50000
>             emtol             =100
>
>
>             nstxout		= 100		; save coordinates every 0.2 ps
>             nstvout		= 100		; save velocities every 0.2 ps
>             nstenergy	= 100		; save energies every 0.2 ps
>             nstlog		= 100		; update log file every 0.2 ps
>             nstxtcout       = 100
>             xtc_precision   = 100
>
> This was not converged! then increase emtol to 3000
> Terminally it was converged for my mdrun,
> But All of the my output files, for example hnum.xvg(g_hnum), are empty. Why?
>

No clue.  You haven't shown us your commands or proved that there's anything 
useful in your trajectory files (e.g. from gmxcheck) that you're analyzing.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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