Hi Pan Wu, There are two things to distinguish:
1. The reference structure used to remove translational and rotational degrees of freedom 2. The reference against which the deviations (on a per atom base) are calculated that are then squared, averaged and taken the root of (root mean square fluctuation). These two need not be the same. It is common, and most sensible, to calculate the deviations against the average structure, after fitting all structures in the trajectory against a certain reference structure. With option -od the deviations against the reference used for fitting are calculated rather than against the average. You do need a reference for fitting, since otherwise you include overall rotation and translation in the calculation of the RMSF, which you usually wouldn't want. I hope this makes it clear. Cheers, Tsjerk On Wed, Oct 14, 2009 at 9:12 PM, Pan Wu <pan...@duke.edu> wrote: > Yes, I also think the *.tpr after -s maybe the reference state. However, In > this way, why in the manual it says like this? > "With the option -od the root mean square deviation with respect to the > reference structure is calculated" > What about without -od, should there be no reference structure or the > reference structure is taken as average over the trajectory? > Thanks! > >>Pan Wu wrote: >>> Hi everyone, >>> Thank you for answering my former questions, it really help me, the >>> new gmx-er a lot~ >>> Here is another question about reference state of RMSF. >>> In the manual, it shows "g_rmsf computes the root mean square >>> fluctuation (RMSF, i.e. standard deviation) of atomic positions >>> after (optionally) fitting to a reference frame". So in this way, can I >>> choose the reference frame from *.tpr file or the coordinate average >>> over the whole trajectory? If Gromacs can, how? >> >>I believe the reference structure is taken from whatever structure file is >> given >>to the -s flag, so in principle you could provide any frame from the >> trajectory, >>as well as the initial one, or some average structure (from, i.e. g_cluster >> or >>something similar). >> >>-Justin > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
