[gmx-users] Steered MD:Setup box in the pulling vector direction and position restraint for protein?

[Bakary N'tji Diallo]

I want to setup a steered molecular dynamics to pull a ligand out of
protein binding site. I used caver to determine an ‘optimal’ pulling
direction for the protein-ligand complex. Now I am to enlarge the
simulation box in that direction.

For now, this is the command I am using:

gmx editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
-5.8 12.2 -6

And getting the following box:
https://drive.google.com/open?id=1SCjMyM-Wo-bKTMRSX9Iz1xwbISTLKIfc

But I would like to enlarge in the direction of the blue arrow on the left.
(The arrow was drawn in VMD using the following coordinates {0 0 0} {-584
1220 -65} and would like to enlarge the simulation box in the same
direction)

The second question is related to this post:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-November/109250.html

It seems like it’s not appropriate to pull to use a position restraint for
the protein. How can one deal properly with the protein?

-- 

Bakary N’tji DIALLO

PhD Student (Bioinformatics) <http://linkedin.com/in/bakarydiallo>, Research
Unit in Bioinformatics (RUBi) <https://rubi.ru.ac.za/>

Mail: diallobakary4 at gmail.com |  Skype: diallobakary4

Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14