[gmx-users] Re: Ask for a question

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.

Most of your questions can be answered by reading molecular modeling textbooks 
or review articles about pulling.  Some of this information is also in the 
manual, so you've certainly missed it.

I would also recommend you read through the COM pulling tutorial I wrote.

http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

Please post any further questions to the list.

-Justin

zhongjin wrote:
> Hello Justin Lemkul,
>      I am sorry to trouble you, but I want to ask some questions about COM pulling in GMX 4.5.1.
>      pull_init1 is the distance between the COMS of reference group and pull group? pull_start = yes means add the COM distance of the starting conformation to pull_init,but 
> what is  the COM distance of the starting conformation? pull_rate1 is whose rate?
> How to select the eference group? How is the pulling force caculated,and the relationship
> between pulling force and the coordinats of  reference group and pull group? I am sorry to ask your so many questions. I have read the GMX manual, but I am very confused.Thanks a lot!
> 
>  Best wishes!
> 
> Zhongjin He
>     
>      
> 
> 
>       
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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