I would like to calculate the RMS fluctuations of residues in an active site, using the following command and options:
g_rmsf -f x16traj.trj -s x16topol.tpr -n index2.ndx -b 1000 -res -o rmsf.xvg -od rmsdev.xvg When the program asks me to "Select group(s) for root mean square calculation", I select the appropriate group number. This gives me rmsf.xvg and rmsdev.xvg files which only contain values for the residues specified in the group I selected. I am focusing on rmsf.xvg, as that has the RMS fluctuation data. I have groups defined for the entire active site, as well as several sub-regions of it. Several residues occur in more than one sub-region. I notice that the values I get for RMSF for the same residue differ, depending on which group I have chosen. (i.e. value for a given residue, when the whole pocket is selected as the group, is different from when I only select a sub-pocket containing that residue). Is g_rmsf somehow referring the coordinates of this residue's atoms to a constantly-changing reference frame? It seems to me that the residue's RMSF(as an average of the RMSF of its atoms) should only be in reference to the average position of its atoms, and not dependent upon some external "frame". Should I just use the whole protein as the reference, and extract the residue values of interest by hand? Thanks, Keith ============================ Keith D. Ball, PhD Staff Scientist Catalyst Biosciences 290 Utah Ave S. San Francisco, CA 94080 650-266-8661 (phone) 650-871-2475 (fax) [EMAIL PROTECTED] http://www.catbio.com ============================
_______________________________________________ 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
