Yes that should be possible without big problems. The Gromacs manual and Wiki pages about how to build a topology is a good starting point.
Then you could try the gromacs program x2top to generate a topology, or the Prodrg2 server. Andreas > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Sascha Rehm > Sent: 14 August 2008 12:03 > To: gmx-users@gromacs.org > Subject: [gmx-users] flexible organic solvents > > Dear Gromacs users, > > I simulate proteins with different organic solvents like toluene, > cyclohexane or isopentane. Right now, I used rigid body models for these > solvents, made and simulated with Amber. For my future work, I unse > Gromacs and need to rebuild these solvents. > > Can I build a cyclohexane model, which is more flexible and can change > from chair conformation to boat conformation and vice versa? And how do > I build a non-rigid Isopentane with internal degrees of freedom? > > Hope, this is not a stupid questions, but I searched quite a while the > mailing list and also google, but did nearly find nothing about other > common (flexible) solvents. > Can someone give me a hint, which keywords I should use to search or > where I can find some informations/tutorials/explanations? > > Thanks a lot, > > Sascha > _______________________________________________ > 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 _______________________________________________ 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
