[gmx-users] Minimization Problems

[Mark Abraham]

On 2/02/2012 3:42 PM, lina wrote:
> On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling<selingal at msu.edu>  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.
>>
>> Can anyone find anything glaringly wrong with my .mdp?
>>
>> 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
> it's more about your .gro file (system), less about the .mdp file.

Can be either. Integration from a silly starting point (.gro) can be 
unstable, as can integration of a silly Hamiltonian (partly due to .mdp).

Mark