[gmx-users] pull.pdo AFM force
soren.enemark at polimi.it
Wed Mar 15 16:29:43 CET 2006
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?
Quoting Emily Walton <ewalton at MIT.EDU>:
> > 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 at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
This mail sent through IMP: http://horde.org/imp/
More information about the gromacs.org_gmx-users