[gmx-users] system is exploding

[Baofu Qiao]

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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>>     
>   


-- 
************************************
 Dr. Baofu Qiao
 Institute for Computational Physics
 Universität Stuttgart
 Pfaffenwaldring 27
 70569 Stuttgart

 Tel: +49(0)711 68563607
 Fax: +49(0)711 68563658