Hi, The reference is used for fitting. The RMSF is calculated with respect to the average (fitted) structure, unless you explicitly specify that deviations from the reference should be used.
Cheers, Tsjerk On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham <[email protected]> wrote: > On 16/02/2011 3:44 PM, [email protected] wrote: >> >> Dear all, >> >> I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms >> with reference to the average structure between 5-10 ns of a total of 10 ns >> simulation as below; >> g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 10000 ?o rmsf.xvg >> >> My understanding of the RMSF is as follows; >> >> RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) >> >> where T is the time over which one wants to average, and Xi is the >> reference position of particle i, which is the time-averaged position of the >> same particle i. >> What I am confused is whether g_rmsf takes the reference structure from >> the structure file (-s), which in my case, the md.tpr and NOT the time >> averaged position over the specified time? > > It does take the reference structure from -s. Whether you actually want the > RMSF from the non-physical time-averaged structure is up to you. IIRC you > might be able to get such an average from g_cluster. > > Mark > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
