[gmx-users] combining gromos96 (43a2) and berger lipid force field
I want to use the gromos96 force field for the protein, and Tieleman's Berger force field for the lipids. How do I combine force fields or construct a topology. I have different topologies for the lipids and the protein ready. However combining them would probably lead to errors as I cannot include both the ffG43a2 and the ffgmx force fields in the same topology ? Thanks for the help, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ 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] combining gromos96 (43a2) and berger lipid force field
The quick answer would be to look at the ffgmx forcefield, and the ffgmx/Berger hybrid that can be obtained (either from Tieleman or the Gromacs website, I forget) and work out how the former was incorporated into the latter. Then replicate that for ffG43a2. Not necessarily simple or even valid, but that's MD for you. - Original Message From: maria goranovic [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, November 7, 2007 7:24:11 PM Subject: [gmx-users] combining gromos96 (43a2) and berger lipid force field I want to use the gromos96 force field for the protein, and Tieleman's Berger force field for the lipids. How do I combine force fields or construct a topology. I have different topologies for the lipids and the protein ready. However combining them would probably lead to errors as I cannot include both the ffG43a2 and the ffgmx force fields in the same topology ? Thanks for the help, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] combining gromos96 (43a2) and berger lipid force field
maria goranovic wrote: I want to use the gromos96 force field for the protein, and Tieleman's Berger force field for the lipids. How do I combine force fields or construct a topology. I have different topologies for the lipids and the protein ready. However combining them would probably lead to errors as I cannot include both the ffG43a2 and the ffgmx force fields in the same topology ? See http://wiki.gromacs.org/index.php/Force_Fields Since you've only recently chosen gromos96, how about instead choosing a forcefield for which lipid parameters have been developed in concert? See the literature for ideas on what works here. 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
