Re: [gmx-users] center of mass and box co-ordinates

[Justin Lemkul]

On 5/7/13 1:05 AM, Arunima Shilpi wrote:

Hello Justin sir

In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
the criteria used to determine the coordinates of center of mass and box
size which you have takes as

editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
6.560 4.362 12



The protein complex is centered in x and y, and the z-dimension provides 
sufficient space to allow for pulling of 5 nm.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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 listgmx-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

[gmx-users] center of mass and box co-ordinates

[Arunima Shilpi]

Hello Justin sir

In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
the criteria used to determine the coordinates of center of mass and box
size which you have takes as

editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
6.560 4.362 12



-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
--
gmx-users mailing listgmx-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