Re: Re: [gmx-users] RMSF reference state?
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 listgmx-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
Re: Re: [gmx-users] RMSF reference state?
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 listgmx-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
Re: [gmx-users] RMSF reference state?
Pan Wu 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? You're talking about two separate calculations. Using -od calculates some sort of RMSD. If you do not use -od, then the standard output (-o) is RMSF, using the fitting described (unless you use -nofit). -Justin 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 listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
Re: [gmx-users] RMSF reference state?
Hi, Actually, Justin is completely right (and I should've checked g_rmsf -h). -od calculates the RMSD from the structure in the frame against the structure in the topology file. This does not nullify the statements regarding references for fitting and references for deviations though :p Cheers, Tsjerk On Wed, Oct 14, 2009 at 9:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Pan Wu 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? You're talking about two separate calculations. Using -od calculates some sort of RMSD. If you do not use -od, then the standard output (-o) is RMSF, using the fitting described (unless you use -nofit). -Justin 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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 listgmx-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
Re: [gmx-users] RMSF reference state?
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 Thank you in advance! -- Sincerely = Pan Wu Graduate Student in Department of Chemistry Duke University 124 Science Drive 5301 French Family Science Center Durham, NC 27708 Phone: (919) 660-1583 = ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
