[gmx-users] time step in gromacs 3.3

[Qing Zhu]

Yang Ye wrote:

> Qing Zhu wrote:
>
>> Hi David
>>
>> I tried to run 3.2.1 tpr with 3.3 using 3 fs as the time step, but 
>> the simulation still crashed after several thousand steps. I have no 
>> idea why there is huge differece between 3.2.1 tpr and 3.3 tpr, 
>> because all the initial conditions are the same except the gromacs 
>> version. Any suggestion?
>
> decrease the time step?

That's the thing I am curious about. With 3.2.1 I can even use 4 fs as 
the time step, but with 3.3  3 fs would make the simulation crash.

>>
>> Thanks
>> Qing Zhu
>>
>> David wrote:
>>
>>> On Fri, 2005-11-04 at 16:01 -0600, Qing Zhu wrote:
>>>  
>>>
>>>> Hi David,
>>>>
>>>> What I did is to run 3.2.1 tpr files with 3.2.1, and run 3.3 tpr 
>>>> files with 3.3.
>>>>   
>>>
>>> Try 3.2.1 tpr with 3.3
>>>
>>>  
>>>
>>>> The results of gmxcheck have hundreds of pages, and I don't know 
>>>> what could I get from gmxcheck.
>>>>   
>>>
>>> See whether the difference is in the tpr or in mdrun.
>>> If you have hundreds of page (pipe it through more) it may mean that 
>>> you
>>> are using a different force field, different coordinate/velocities 
>>> which
>>> means you can  not compare the simulations.
>>>
>>>
>>>  
>>>
>>>> Thanks
>>>> Qing Zhu
>>>>
>>>>
>>>> David wrote:
>>>>
>>>>   
>>>>
>>>>> On Fri, 2005-11-04 at 15:25 -0600, Qing Zhu wrote:
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>> Hi, everyone
>>>>>>
>>>>>> I tried to run lipid membrane simulations by setting the time 
>>>>>> step to be 3 fs using gromacs-3.3,  and my simulations always 
>>>>>> crashed after a short time unless I changed the time step back to 
>>>>>> 2 fs. But if I run the same lipid membrane simulations using 
>>>>>> gromacs-3.2.1, I can even use 4 fs as time step and the 
>>>>>> simulations runs fine. It is not a big problem for me, but I am 
>>>>>> just curious that why gromacs-3.3 is so critical about the time 
>>>>>> step. Any one has an idea?
>>>>>>  
>>>>>>       
>>>>>
>>>>> Did you try running your 3.2.1 tpr file with 3.3 ? Did you compare 
>>>>> 3.2.1 and 3.3 tpr files (using gmxcheck)?
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>> Thanks
>>>>>> Qing Zhu
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>>>>>>  
>>>>>>       
>>>>>
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>>
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>
> -- 
> /Regards,/
> Yang Ye
> /Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884
> /
>
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Thanks
Qing Zhu