Thanks for your reply, >>Chris The test I ran was just rotating a side chain of an amino acid residue over one of its dihedral angle 360 degrees with dihre_fc = 8000.
I originally thought fc = 8000kJ/mol unit^2 would give fluctuation of about the half the unit size since I use fc = 8000kJ/mol nm^2 for 0.5A spacing. But, after I thought twice about it, it would be fc = 80kJ/moml nm^2, for 0.5nm spacing... So, after I realized that, kJ/mol rad^2 made sense to me and my test run's fluctuation (about several degress = 1/20 rad = about 3 degrees) >>David I think Chris meant "my test run" :) It's good to hear that your implementation can produce a reasonable PMF profile. I hope mine will, too. Thanks again, Ryogo On Tue, 23 Jan 2007 18:26:59 -0500, Chris Neale wrote: > Quoting manual-3.3 page 58 > "Note that in the input in topology files, angles are given in > degrees and force constants in kJ/mol/rad2." > > I assume here that force constants refers to dihre_fc. However, > although the test PMF's that I have generated for the alanine > dipeptide have the correct shape, the WHAM-PMF magnitudes that are > too large by a factor of 10-20. > > Please describe the test that you ran. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
