Re: [gmx-users] Regarding g_order

2013-08-02 Thread Justin Lemkul
On 8/2/13 2:04 AM, Venkat Reddy wrote: Thanks Justin for the quick reply. I am simulating a protein with bound lipids. I am in a dilemma to choose the direction of the normal to calculate order parameter. In your *Membrane-protein *simulation tutorial, you have chosen normal to the bilayer alon

Re: [gmx-users] Regarding g_order

2013-08-01 Thread Venkat Reddy
Thanks Justin for the quick reply. I am simulating a protein with bound lipids. I am in a dilemma to choose the direction of the normal to calculate order parameter. In your *Membrane-protein *simulation tutorial, you have chosen normal to the bilayer along the z-axis. But in my case, there is no b

Re: [gmx-users] Regarding g_order

2013-08-01 Thread Justin Lemkul
On 8/1/13 12:07 PM, Venkat Reddy wrote: Dear Gmx-users, In the GROMACS site, it has been mentioned that there is a bug (Instead of numbering carbons from 2-17, the numbering starts from 1-16) in g_order program up to, and including, v4.5.4. But when I am using v4.5.5, I am getting the same sort

[gmx-users] Regarding g_order

2013-08-01 Thread Venkat Reddy
Dear Gmx-users, In the GROMACS site, it has been mentioned that there is a bug (Instead of numbering carbons from 2-17, the numbering starts from 1-16) in g_order program up to, and including, v4.5.4. But when I am using v4.5.5, I am getting the same sort of numbering. Is it normal or I should renu