Re: [gmx-users] Problems plotting gyrate.xvg
Oh... So you are using gnuplot? The gyrate.xvg file is xmgrace native, so if you want to plot it with the built-in labels and such use xmgrace -nxy gyrate.xvg; if you want to use gnuplot, then you need to have it filter out all of the lines that have either # and @ symbols at the begining (though with the you should stop otherwise you will have your second plot taken into the first). -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:39 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problems plotting gyrate.xvg Since version 4.6 it is not necessary to do so, it detects it automatically and it did. I didn't have problems obtaining the radius of gyration, I actually have it. I just have problems getting the plot using the command: plot gyrate.xvg using 1:2 with lines 2015-08-18 11:23 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 8/18/15 10:13 AM, Daniela Rivas wrote: Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. One needs to specifically link against VMD's libraries when installing GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD. -Justin 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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] Problems plotting gyrate.xvg
Yes, I'm using gnuplot. I'll give it a try and see if that works. Thanks! 2015-08-18 11:42 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Oh... So you are using gnuplot? The gyrate.xvg file is xmgrace native, so if you want to plot it with the built-in labels and such use xmgrace -nxy gyrate.xvg; if you want to use gnuplot, then you need to have it filter out all of the lines that have either # and @ symbols at the begining (though with the you should stop otherwise you will have your second plot taken into the first). -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:39 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problems plotting gyrate.xvg Since version 4.6 it is not necessary to do so, it detects it automatically and it did. I didn't have problems obtaining the radius of gyration, I actually have it. I just have problems getting the plot using the command: plot gyrate.xvg using 1:2 with lines 2015-08-18 11:23 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 8/18/15 10:13 AM, Daniela Rivas wrote: Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. One needs to specifically link against VMD's libraries when installing GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD. -Justin 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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
Re: [gmx-users] Problems plotting gyrate.xvg
On 8/18/15 10:13 AM, Daniela Rivas wrote: Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. One needs to specifically link against VMD's libraries when installing GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD. -Justin 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Problems plotting gyrate.xvg
On 8/18/15 10:39 AM, Daniela Rivas wrote: Since version 4.6 it is not necessary to do so, it detects it automatically and it did. I didn't have problems obtaining the radius of gyration, I actually have it. I just have problems getting the plot using the command: plot gyrate.xvg using 1:2 with lines By default, GROMACS produces XmGrace-formatted files. It may not open in Gnuplot without some modification. -Justin 2015-08-18 11:23 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 8/18/15 10:13 AM, Daniela Rivas wrote: Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. One needs to specifically link against VMD's libraries when installing GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD. -Justin 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Problems plotting gyrate.xvg
Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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] Problems plotting gyrate.xvg
Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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] Problems plotting gyrate.xvg
Daniela, I believe your issue is the DCD file, as I look at the help for g_gyrate (from 4.6.5), I don't see a compatability with DCD. You could convert it to a pdb and then using g_gyrate and see if that fixes the issue. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:13 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problems plotting gyrate.xvg Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- 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] Problems plotting gyrate.xvg
Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- 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] Problems plotting gyrate.xvg
Since version 4.6 it is not necessary to do so, it detects it automatically and it did. I didn't have problems obtaining the radius of gyration, I actually have it. I just have problems getting the plot using the command: plot gyrate.xvg using 1:2 with lines 2015-08-18 11:23 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 8/18/15 10:13 AM, Daniela Rivas wrote: Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. One needs to specifically link against VMD's libraries when installing GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD. -Justin 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Problems plotting gyrate.xvg
So unless the file is corrupted or empty, this is a gnuplot problem and not a gromacs one. Check inside your gyrate file with a text editor to see if it is correct. On 18/08/15 16:39, Daniela Rivas wrote: Since version 4.6 it is not necessary to do so, it detects it automatically and it did. I didn't have problems obtaining the radius of gyration, I actually have it. I just have problems getting the plot using the command: plot gyrate.xvg using 1:2 with lines 2015-08-18 11:23 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 8/18/15 10:13 AM, Daniela Rivas wrote: Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. One needs to specifically link against VMD's libraries when installing GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD. -Justin 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- 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] Problems plotting gyrate.xvg
http://www.gromacs.org/Documentation/How-tos/Graphing_Data On Tue, Aug 18, 2015 at 4:51 PM Daniela Rivas dani.riva...@gmail.com wrote: Yes, I'm using gnuplot. I'll give it a try and see if that works. Thanks! 2015-08-18 11:42 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Oh... So you are using gnuplot? The gyrate.xvg file is xmgrace native, so if you want to plot it with the built-in labels and such use xmgrace -nxy gyrate.xvg; if you want to use gnuplot, then you need to have it filter out all of the lines that have either # and @ symbols at the begining (though with the you should stop otherwise you will have your second plot taken into the first). -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:39 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problems plotting gyrate.xvg Since version 4.6 it is not necessary to do so, it detects it automatically and it did. I didn't have problems obtaining the radius of gyration, I actually have it. I just have problems getting the plot using the command: plot gyrate.xvg using 1:2 with lines 2015-08-18 11:23 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 8/18/15 10:13 AM, Daniela Rivas wrote: Micholas, My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5. One needs to specifically link against VMD's libraries when installing GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD. -Justin 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov: Daniela, What exact is your input? And what version of gromacs? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Daniela Rivas dani.riva...@gmail.com Sent: Tuesday, August 18, 2015 10:00 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Problems plotting gyrate.xvg Hi, I've been trying to plot the radius of gyration I got using gromacs, but I keep getting the segmentation fault. What does this mean? I have plenty memory (32 TB), so it can't be a memory problem. My trajectory has 4 frames (20 ns simulation) and I'm calculating the radius of gyration of my protein (~7000 atoms). Thanks in advance. Daniela. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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
