[gmx-users] Minimization Problems

[Mark Abraham]

On 2/02/2012 3:36 PM, Alex Seling wrote:
> Hello,
>
> I've recently been having trouble with my simulations blowing up. 
> Specifically,
>
> "This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size"
>
> for a few interactions, with each of them approaching inf.

The usual advice and diagnostic procedure can be found here 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

>
> Can anyone find anything glaringly wrong with my .mdp?

No constraints often requires a time step of 0.0005ps.

Mark

>
> Thanks,
> Alex Seling
>
> title = Minimization of alpha-synuclein
> cpp = /lib/cpp -traditional
> define = -DFLEXIBLE
> integrator = sd
> constraints = none
> tinit = 0
> dt = 0.001
> nsteps = 1000000
> emtol = 0.00001
> emstep = 0.1
> nstcgsteep = 1000
> bd-fric = 0
> nstlog = 50
> nstenergy = 1
> gen_temp = 273
> gb_epsilon_solvent = 78.3
> implicit_solvent = GBSA
> gb_algorithm = Still
> nstcomm = 10
> xtc_precision = 1000
> gen_vel = yes
> nstxtcout = 0
> nstxout = 100
> pbc = no
> energygrps = system
> nstfout = 0
> nstvout = 0
> niter = 20
> nstlist = 10
>
>

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