Re: [gmx-users] Carbon Nanotube Residue
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. See also http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,100/Itemid,26/ for reference what the topology should like like. For some time, I was working with the problem of simulating the CNT by means of GROMACS, and I'll be glad to consult you if you have got any additional questions. Best, Vitaly ___ gmx-users mailing listgmx-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
Re: [gmx-users] Carbon Nanotube Residue
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 listgmx-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 listgmx-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
Re: [gmx-users] Carbon Nanotube Residue
Justin A. Lemkul wrote: 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. I agree, and note that there's some useful material here http://wiki.gromacs.org/index.php/Carbon_Nanotube Mark ___ gmx-users mailing listgmx-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
