[gmx-users] system is exploding

[T.M.D. Graen]

check your custom topology (this is where the error is 99% of the time), 
use qm minimized starting structures, make sure your structure matches 
your topology (atom names,numbers,ordering, etc.), test single molecules 
in vacuum first and/or reduce the step size of your SD minimizer.

On 11/26/2010 11:47 AM, Baofu Qiao wrote:
>
> If you are really sure about the topology, the problem is the initial
> structure. Try to use PackMol to build it.
>
> On 11/26/2010 11:42 AM, Olga Ivchenko wrote:
>> I tried today to run minimization in vacuum for my small molecules. This has
>> the same error.
>>
>> 2010/11/26 Baofu Qiao<qiaobf at gmail.com>
>>
>>
>>> Have you run the energy minimization (or further simulation to optimize
>>> the structure and test the FF) on the small molecule before you added it
>>> into water?
>>>
>>> On 11/26/2010 11:26 AM, Olga Ivchenko wrote:
>>>
>>>> Dear gromacs users,
>>>>
>>>> I am trying to run simulations for small molecules in water. Topology
>>>>
>>> files
>>>
>>>> I created by my self for charm ff. When I am trying to start energy
>>>> minimization I got an error:
>>>>
>>>>
>>>>   Steepest Descents:
>>>>
>>>> Tolerance (Fmax) = 1.00000e+00
>>>>
>>>> Number of steps = 1000
>>>>
>>>>
>>>> That's means my system is exploding. Please can you advice me on this,
>>>>
>>> what
>>>
>>>> I need to check.
>>>>
>>>> best,
>>>>
>>>> Olga
>>>>
>>>>
>>>>
>>>
>>> --
>>> ************************************
>>>   Dr. Baofu Qiao
>>>   Institute for Computational Physics
>>>   Universität Stuttgart
>>>   Pfaffenwaldring 27
>>>   70569 Stuttgart
>>>
>>>   Tel: +49(0)711 68563607
>>>   Fax: +49(0)711 68563658
>>>
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>>
>
>