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