[gmx-users] Can gromacs got average position of a molecule

[Yang Ye]

David van der Spoel wrote:

> qiwenpeng at sinap.ac.cn wrote:
>
>> Dear All:
>>  
>> I use gromacs3.3 to simulate a DNA. After Equilibration I got the 
>> energy of bond is about 240 kj/mol , but the status on an article is 
>> 130 kj/mol .
>>  
>> I think it may be the conformation of the molecule need to be average 
>> over a few ps .
>
> please be more specific. could be due to timestep.

bond energy shall not vary much through out the trajectory. What's your 
zero-point energy (at t=0)? Does it agree?

>
>>  
>> Is there any functions that gromacs has enclude to do this?
>>  
>> Thank you all!!
>>
>>
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>
>

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