I would recommend reading lots of tutorial material and the Gromacs
manual, especially Chapter 5. There are also numerous posts from Chris
Stiles that contain a link to a tutorial he set up a while back for
doing CNT simulations.
The main point is that you need to generate a topology that calls
parameters from an existing force field, not modify a force field or
structure.
-Justin
[EMAIL PROTECTED] wrote:
I'm new to gromacs and the past week or so I've been digging through the
archives so that I can simulate a carbon nanotube. I've been able find
coordinates for the carbon nanotube as well as the parameters for the
force field. My question is:
Do I define the parameters in the force field file or can I do it in pdb
file?
I'm asking because I'm unable to change the force field file, so if I
could just define the carbon nano tube residue in the pdb file that would
help me out a lot.
Thanks,
-John
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
