Can I put constraint on selected bond? Nilesh On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote: > 1. Using freezegrps is not generally a good idea to fix a bond length. > Look at the constraints mechenism better. Or just try a bigger force > constant in topology. > > 2. NPT and freezegrps do not interact correctly, since freezegrps just > freezes any changes of atom positions, so they are not rescaled even if the > box size is changed in NPT. > > 3. Anyway, I think you have defined incorrect groups if your atoms of > interest are still movable. Check a diffusion constant of your bonded > atoms, it should be zero in the case of freezegrps. > > Dr. Vitaly Chaban > > > > > >> I am trying to freeze a bond (3.5 A) in my system. I used the index >> file to define group and I added this two lines in my .mdp file. >> >> freezegrps = PA NE freezedim = Y Y Y Y Y Y >> >> I used g_dist to verify the distance between the freezing atoms. During >> the NVT simulation the distace is around 3.449 A and its constant >> though out the simulation. For NPT simulation the distance varies from >> 3.449 to >> 3.1. >> Can you tell why distance changes in NPT not in NVT. >> How can I freeze a bond om NPT simulation? >> >> > -- > gmx-users mailing list [email protected] > http://lists.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 > > >
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