[gmx-users] Re: how is the pulling force measured

I would like to give my understanding of the pulling method. I don't look into the code either. I am not sure if my understanding is right. Any correction is welcome. I think the reference point connecting with the pulled group by spring is an COM offset of the reference group. The reference

[gmx-users] Re: how is the pulling force measured

Hi Alex, I read the manual but I got confused with the details. My pull_geometry = position with pulling direction along y. I am trying to dissociate two interacting proteins. So I set the last amino acid of one protein as my reference group and the last amino acid of the other protein as the

[gmx-users] Re: how is the pulling force measured

2013/4/30 kim2811 [via GROMACS] ml-node+s5086n5007778...@n6.nabble.com Hi Alex, I read the manual but I got confused with the details. My pull_geometry = position with pulling direction along y. I am trying to dissociate two interacting proteins. So I set the last amino acid of one protein

[gmx-users] Re: how is the pulling force measured

I never looked into the code, but i understanded it the following way (for pull_geometry = distane, direction, position). For the pulling the reference group is held fixed and the force is applied to the pulled group. Since the reference group an move during the rest of the simulation (all

Aw: [gmx-users] Re: how is the pulling force measured

I appologise, I meant defined at the same time without complaining, not just either direction. Gesendet:Montag, 29. April 2013 um 22:23 Uhr Von:lloyd riggs lloyd.ri...@gmx.ch An:S. Watkins gmx-users@gromacs.org Betreff:Aw: [gmx-users] Re: how is the pulling force measured Dear All, Doing

Re: Aw: [gmx-users] Re: how is the pulling force measured

term. I have a toy test case that shows this. -Justin *Gesendet:* Montag, 29. April 2013 um 22:23 Uhr *Von:* lloyd riggs lloyd.ri...@gmx.ch *An:* S. Watkins gmx-users@gromacs.org *Betreff:* Aw: [gmx-users] Re: how is the pulling force measured *Dear All,* *Doing a water/temp energy minimization

[gmx-users] Re: how is the pulling force measured

kim2811 wrote Hi, I am not sure if I quite understand what reference group and pulling group mean in COM pulling. For the version GROMACS 4.X, I specified in my .mdp file the pull_ngroup = 1, and then I have my pull_group0 and pull_group1. Am I right in saying that the pull_group0 is fixed

Aw: [gmx-users] Re: how is the pulling force measured

Dear All, Doing a water/temp energy minimization just for a figure with a large molecule that has several connected parts, I ran into a bizzar question. So I found its possible by accident to define improper dihedrails forwards and backwards without gromacs complaining, such as atom 1 2 3 4