Hey Chris,
It is actually not necessary to go to the code. You can do that by compiling a version of gromacs including the plumed path for free energy calculations. Amogst the several collective variables included there there is gyration radius. Regards Felipe ----Mensaje original----De: chris.neale@utoronto.caFecha: 29-mar-2012 10:50Para: <gmx-users@gromacs.org>Asunto: [gmx-users] Umbrella sampling along Radius of gyrationIt is not clear to me how one would do this with MD. The only thing that I can think of doing in gromacs is to create a virtual particle that is placed at the center of the protein and then apply forces along the vector from this virtual atom to each of the Ca atoms. You would need to modify the gromacs source code so that the Rg was calculated at each step and the magnitude of each force is scaled appropriately such that you get a harmonic potential about the desired value of Rg. It should be easier to do with MC (although that's a ways off for gromacs unless I've missed something).Some people appear to have done exactly what you want with MD. I presume that they used charmm.http://www.pnas.org/content/94/19/10161.long (and their reference 22).Chris.-- original message --Hi, Is there any way in gromacs to use radius of gyration of a polymer as reaction coordinate for umbrella sampling ?ThanksSanku-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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