Farzad, The force constant is up to you to define in the .ppa file you create for umbrella sampling.
I ask the question about the 0.5 term because I am using Grossfield¹s WHAM algorithm and it assumes that the biasing potential used has a 0.5 in front, but I know for example CHARMM does not include the 0.5 and I just need to know if this is also the case with gromacs. Thank you. -Dina On 12/17/07 12:34 AM, "Farzad Molani" <[EMAIL PROTECTED]> wrote: > Hi dear > I think it has got 0.5 in equation. > U=0.5*K(r-b)2 > but I dont knoe how do I get K please help me > > dtmirij <[EMAIL PROTECTED]> wrote: >> Hello everyone, >> >> I would like to know does the harmonic biasing potential for running >> umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term >> incorporated into the force constant value that we specify? >> On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2. >> >> Thank you in advance. >> -Dina >> >> >> _______________________________________________ >> 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 > > > > > Never miss a thing. Make Yahoo your homepage. > <http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs> > > _______________________________________________ > 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
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