[gmx-users] time step in gromacs 3.3

[Yang Ye]

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.
>  
>
To check whether tpr's problem
use 3.3's gmxcheck -s1 {3.2.1}.tpr -s2 {3.3}.tpr

>
>  
>
>>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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>>    
>>

-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/