Hi Emily, sometimes one can be quite lucky..:) I have just done a few simulations in which I try to pull two molecules apart. I want to calculate the force as a function of intermolecular distance, and I just saw your post. Can I ask you for the script that you mentioned?
Cheers -Søren Quoting Emily Walton <[EMAIL PROTECTED]>: > > Hi all > > I have a short question. Could you please tell me what do the > > columns in pull.pdo (output file from AFM) stand for. Is there a > > simple way to obtain forces from AFM pulling? Thank you for help. > > Michal > > > > As an example, with one pulling group, and pulling in 3D, the output > columns read: > > Time, Reference group X, Reference group Y, Reference group Z, Pull > Group X, Pull Group Y, Pull Group Z, Spring X, Spring Y, Spring Z > > for a total of 10 columns. > > If you didn't pull in 3D, you'll only get output for the dimensions > where pulldim was set to Y in your .ppa file. I'm not sure how > multiple pull groups are handled. > > I have a script to calculate the forces for pull runs using only one > pull group in 3 dimensions that I can share on request. > > -Emily Walton > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php