[gmx-users] Umbrella sampling along Radius of gyration

felmerino at uchile.cl felmerino at uchile.cl
Thu Mar 29 17:13:08 CEST 2012

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.




----Mensaje original----De: chris.neale at utoronto.caFecha: 29-mar-2012 10:50Para: <gmx-users at 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 at 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-request at gromacs.org.Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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