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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
