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 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. > Ah. I think it would be wiser to use pull_geometry=distance, so that the two groups (0 and 1, reference and pulled) are connected by a spring. It might also be better to use groups bigger than one amino acid, but I guess that depends on what you want to accomplish. A very useful tutorial in which two interacting peptides are separated can be found here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html > > 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? > I'm no expert and will have to leave this question unanswered. Sorry. > > "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. > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://gromacs.5086.x6.nabble.com/how-is-the-pulling-force-measured-tp5007769p5007778.html > To unsubscribe from how is the pulling force measured, click > here<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=5007769&code=YWxleC5iam9ybGluZ0BnbWFpbC5jb218NTAwNzc2OXwxNTY0MDc3NjU4> > . > NAML<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- View this message in context: http://gromacs.5086.x6.nabble.com/how-is-the-pulling-force-measured-tp5007769p5007781.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
