[gmx-users] Re: Ask for a question

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:04:59 CEST 2010

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.


Please post any further questions to the list.


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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list