Re: [gmx-users] the a.u. unit in the RMS distribution graph
Thank you Justin, that saved me a lot of time. Best, Lalehan On Sun, Dec 1, 2019 at 3:45 PM Justin Lemkul wrote: > > > On 12/1/19 3:48 AM, Lalehan Ozalp wrote: > > Hello Christian, thank you for providing the patch. However I wonder if > > there is an easier way to convert a.u to frequency - as I need to install > > GROMACS from the start to install the patch. One more thing, I used > version > > 5.0, not 2019, and the patch is written for the version 2019. > > Change the axis label in the .xvg file with a text editor or re-label it > in XmGrace once the data are plotted. You don't need to run the analysis > again with the updated code. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
On 12/1/19 3:48 AM, Lalehan Ozalp wrote: Hello Christian, thank you for providing the patch. However I wonder if there is an easier way to convert a.u to frequency - as I need to install GROMACS from the start to install the patch. One more thing, I used version 5.0, not 2019, and the patch is written for the version 2019. Change the axis label in the .xvg file with a text editor or re-label it in XmGrace once the data are plotted. You don't need to run the analysis again with the updated code. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Christian, thank you for providing the patch. However I wonder if there is an easier way to convert a.u to frequency - as I need to install GROMACS from the start to install the patch. One more thing, I used version 5.0, not 2019, and the patch is written for the version 2019. Thank you again, Lalehan On Fri, Nov 29, 2019 at 7:34 PM Christian Blau wrote: > Hello Lalehan and Justin, > > > Thanks for the suggestion! The following patch : > https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that. > > > Best, > Christian > > On 2019-11-29 14:23, Justin Lemkul wrote: > > > > > > On 11/29/19 7:18 AM, Christian Blau wrote: > >> Hello Lalehan, > >> > >> > >> a.u. stands for "arbitrary units". > >> > >> The rmsd-dist contains a histogram over the distribution of rmsd > values, you can read the a.u. as counts per > >> length-interval. > >> > > > > I would suggest that all histograms that GROMACS produces actually be > labeled reasonably in the code - using a.u. is > > itself arbitrary because it has multiple possible meanings. If it's a > raw histogram, we should be using "Frequency" > > and if normalized, "Probability." > > > > -Justin > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Lalehan and Justin, Thanks for the suggestion! The following patch : https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that. Best, Christian On 2019-11-29 14:23, Justin Lemkul wrote: On 11/29/19 7:18 AM, Christian Blau wrote: Hello Lalehan, a.u. stands for "arbitrary units". The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per length-interval. I would suggest that all histograms that GROMACS produces actually be labeled reasonably in the code - using a.u. is itself arbitrary because it has multiple possible meanings. If it's a raw histogram, we should be using "Frequency" and if normalized, "Probability." -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Justin, thank you for the response. In that case I should use "frequency" if I plan to take it the way it is. Thanks, On Fri, Nov 29, 2019 at 4:25 PM Justin Lemkul wrote: > > > On 11/29/19 7:18 AM, Christian Blau wrote: > > Hello Lalehan, > > > > > > a.u. stands for "arbitrary units". > > > > The rmsd-dist contains a histogram over the distribution of rmsd > > values, you can read the a.u. as counts per length-interval. > > > > I would suggest that all histograms that GROMACS produces actually be > labeled reasonably in the code - using a.u. is itself arbitrary because > it has multiple possible meanings. If it's a raw histogram, we should be > using "Frequency" and if normalized, "Probability." > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
On 11/29/19 7:18 AM, Christian Blau wrote: Hello Lalehan, a.u. stands for "arbitrary units". The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per length-interval. I would suggest that all histograms that GROMACS produces actually be labeled reasonably in the code - using a.u. is itself arbitrary because it has multiple possible meanings. If it's a raw histogram, we should be using "Frequency" and if normalized, "Probability." -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Christian! Thank you for the valuable information :) Best, Lalehan On Fri, Nov 29, 2019 at 3:18 PM Christian Blau wrote: > Hello Lalehan, > > > a.u. stands for "arbitrary units". > > The rmsd-dist contains a histogram over the distribution of rmsd values, > you can read the a.u. as counts per > length-interval. > > > Best, > > Christian > > On 2019-11-29 12:57, Lalehan Ozalp wrote: > > Hello everyone, I ran a cluster analysis for a 10 ns simulation and > > produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg > file, > > I see "a. u." in the y axis which I couldn't entirely understand. Is it > > supposed to stand for atomic unit for length or mass or something else? I > > provide the file as an example. > > > > Thank you in advance. > > > > Lalehan > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Lalehan, a.u. stands for "arbitrary units". The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per length-interval. Best, Christian On 2019-11-29 12:57, Lalehan Ozalp wrote: Hello everyone, I ran a cluster analysis for a 10 ns simulation and produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg file, I see "a. u." in the y axis which I couldn't entirely understand. Is it supposed to stand for atomic unit for length or mass or something else? I provide the file as an example. Thank you in advance. Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] the a.u. unit in the RMS distribution graph
Hello everyone, I ran a cluster analysis for a 10 ns simulation and produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg file, I see "a. u." in the y axis which I couldn't entirely understand. Is it supposed to stand for atomic unit for length or mass or something else? I provide the file as an example. Thank you in advance. Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
