[gmx-users] constant force pulling

Hi, I am trying to pull/separate a protein dimer by applying constant force in my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set my simulation to run for 5 ns. However, after only 251 ps, I got this

[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 pul

[gmx-users] how is the pulling force measured

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 and only the pull_gro

[gmx-users] any other criteria for h-bond?

Hi, is there any other criteria in determining a hydrogen bond? i know that in order for a bond to exist, donor-acceptor distance should be less than or equal 3.5A and A-D-H angle less than or equal 30deg. I used g_sgangle to measure the angle A-D-H of two hydrogen bonds identified when I determine