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 pulled group. Now, I don't know exactly how to interpret what reference group and pulled group mean, and what is their difference; since in the manual it says 'there is no difference in treatment of the reference and pulled group (except with the cylinder geometry).' Also, it says that measured force output is the force of the pulled group.
So basically, I am trying to visualize how the system works. Using the pull_geometry stated above, are the two groups (reference and pulled) attached to two virtual springs? Will this statement be correct? "Force was applied by moving the clamped ends of the two springs (i = 1, 2) in opposite directions with constant velocity v to positions Zi(t) = zi(0) + vt, where zi(0) is the initial position of the end of the molecule. The forces fi(t) at the two ends were measured at every time step using the relationship fi(t) = k (zi(t) − Zi(t))." I hope my questions make sense. Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/how-is-the-pulling-force-measured-tp5007769p5007778.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-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
