Re: [gmx-users] Few queries about microsecond long simulations
Hi, This are all questions that mostly only you can answer. On 18/08/15 12:42, anu chandra wrote: Dear Gromcas users, I am planning to do microsecond long simulation of membrane-protein system and I have ~100,000 atoms in the systems. Since I am trying for microsecond long simulations and I have a quiet large system, it can generate large amount of data and in this regard I would like to clarify few queries before continue the simulations. My queries are, 1. How often I should save the trajectories? In general, I have seen that mostly use 2ps interval for saving trajectories, as shown below. Will it be safe if I use 10ps ( 5000 steps ) interval for saving trajectories? nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps The files you create and the frequency with which you write them depends only on what you want to measure in the end. In principle, you want to save every couple of decorrelation times, for whatever property interests you. I assume that since you want a microsecond-long simulation then you are going for a slow process and therefore you don't need so frequent saving. Just as a comparison, for one of my simulations (~550k atoms, 1 µs) I save the coordinates every 40 ps which gives me a final xtc of ~50Gb of space. 2. How safe if I just write only the compressed .xtc file of the trajectories and not the .trr file during the production run? If its safe, how can I tell mdrun not to write the trr file? 3. Do I really need the trr file for any MD analysis? Again, you should know if you need the velocities later, or if need a high precision for the coordinates. If you don't, then leave the mdp as, nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 1000 nstxtcout = 1000 Many thanks in advance Anu -- 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.
[gmx-users] Few queries about microsecond long simulations
Dear Gromcas users, I am planning to do microsecond long simulation of membrane-protein system and I have ~100,000 atoms in the systems. Since I am trying for microsecond long simulations and I have a quiet large system, it can generate large amount of data and in this regard I would like to clarify few queries before continue the simulations. My queries are, 1. How often I should save the trajectories? In general, I have seen that mostly use 2ps interval for saving trajectories, as shown below. Will it be safe if I use 10ps ( 5000 steps ) interval for saving trajectories? nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps 2. How safe if I just write only the compressed .xtc file of the trajectories and not the .trr file during the production run? If its safe, how can I tell mdrun not to write the trr file? 3. Do I really need the trr file for any MD analysis? Many thanks in advance Anu -- 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] Error: 'mdrun_mpi' is not a GROMACS command.
On 8/18/15 8:08 AM, anu chandra wrote: Dear Gromcas users, I just expericend an error while running mpi version of Gromcas on a 64 processors in a cluster. The command I used for running mdrun is as follows, mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2 But, unfortunately the run terminated with following error message. Can anyone help me to figure out what is gone wrong here? --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: 'mdrun_mpi' is not a GROMACS command. - The _mpi suffix only applies to the gmx binary, so it should be gmx_mpi mdrun ... -Justin -- == 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] Error: 'mdrun_mpi' is not a GROMACS command.
Dear Gromcas users, I just expericend an error while running mpi version of Gromcas on a 64 processors in a cluster. The command I used for running mdrun is as follows, mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2 But, unfortunately the run terminated with following error message. Can anyone help me to figure out what is gone wrong here? --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: 'mdrun_mpi' is not a GROMACS command. - Many thanks Anu -- 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] tabulated potential - problem
Dear all, I have a question about the handling of the tabulated interactions. I am using tabulated potentials for my simulations. With grompp there is no problem, i.e. no error messages. Running mdrun produces: Fatal error: A tabulated bond interaction table number 1 is out of the table range: r 13.532542, between table indices 135325 and 135326, table length 6 I really do not understand this error. Considering my system it seems to be senseless. The value for r in the first column of my table is ranged from 0 to 6nm with a step size of 0.001nm. My box size is 6nm. So how is it possible that a bonded interaction is greater than the box itselfs? I am actually thinking, that it should be enough that the table is ranged from 0 to 2 or 3nm as the interaction is a bonded one. Or does this error message only occur, because of the fact that my system is crashing - so as a result from an other error in my files? Tank you very much in advance. Best, Liz -- 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] Few queries about microsecond long simulations
Hi Anu, 1) It really depends on what kind of analysis you are doing. If you are, for example, studying bio-molecular interactions that take place over microsecond long timescales then saving trajectories every 200-500 ps is advisable. I myself do receptor-membrane atomistic simulations with a saving frequency of 500 ps. You don't really need saving which is as frequent as 10 ps. 2), 3) Whereas .xtc trajectories contain only the coordinates, .trr trajectories contain both coordinates as well as velocities. So unless you are going to do any analysis which involves the velocities of atoms/particles, its safe to not write-out the .trr file. Still you are never really sure if you are going to require velocities or not and so it's best to write out the .trr file as well. On Tue, Aug 18, 2015 at 4:30 PM, Felipe Merino felipe.mer...@mpi-dortmund.mpg.de wrote: Hi, This are all questions that mostly only you can answer. On 18/08/15 12:42, anu chandra wrote: Dear Gromcas users, I am planning to do microsecond long simulation of membrane-protein system and I have ~100,000 atoms in the systems. Since I am trying for microsecond long simulations and I have a quiet large system, it can generate large amount of data and in this regard I would like to clarify few queries before continue the simulations. My queries are, 1. How often I should save the trajectories? In general, I have seen that mostly use 2ps interval for saving trajectories, as shown below. Will it be safe if I use 10ps ( 5000 steps ) interval for saving trajectories? nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps The files you create and the frequency with which you write them depends only on what you want to measure in the end. In principle, you want to save every couple of decorrelation times, for whatever property interests you. I assume that since you want a microsecond-long simulation then you are going for a slow process and therefore you don't need so frequent saving. Just as a comparison, for one of my simulations (~550k atoms, 1 µs) I save the coordinates every 40 ps which gives me a final xtc of ~50Gb of space. 2. How safe if I just write only the compressed .xtc file of the trajectories and not the .trr file during the production run? If its safe, how can I tell mdrun not to write the trr file? 3. Do I really need the trr file for any MD analysis? Again, you should know if you need the velocities later, or if need a high precision for the coordinates. If you don't, then leave the mdp as, nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 1000 nstxtcout = 1000 Many thanks in advance Anu -- 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. -- Best Regards, Ganesh Shahane -- 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] Umbrella sampling and transmission coefficient
Dear user, I did umbrella sampling simulation and get PMF profile of my system. In order to calculate the rate constant I need to estimate the transmission coefficient. Do you have any advice about getting the transmission coefficient in GROMACS? Best -- 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] add NaCl
Hi; I've already converted topology and coordinate files which were generated with amber tools to .gro format. But now, when I want to add 100Mm NaCl to the system I get this error: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'c6m1_GMX.top' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I think that it cannot recognize the solvent. How can I fix it? Thank you, Mohammad -- 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] Thread, Multiple gpu, and sharing node
Dear Users, Hi. The system has about 3k atoms, and I used a rhombic dodecahedron box. The node in the cluster has 2 sockets and 12 cores per socket. (24 sockets in total) It also has 4 gpu. Will I waste cpu time, if I run with all 24 cores and assign 1 gpu to 3 cores? Should I compile for mpi? Alternatively, I can run with just 12 cores and assign 1 gpu to every 3 cores. The remaining 12 cores and 2 gpu will be used by another user. Which way is a more efficient use of time per cpu core? Thank you. -- 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] Tesla K40 and K80 performance for Gromacs
Hi gromacs users, Our lab decides to buy some exclusive computational resources for MD using gromacs. The HPC center in our university offers 2 options. I guess some of you are using K80 GPU right now so I'd like to hear your suggestions/experiences about it. option 1 (Tesla K40): * Dual Intel Xeon E5-2680 v3, 12C, 2.5GHz, 2133MHz RAM, 120W * 128GB, DDR4-2133 ECC, 2R (8 x 16GB) * 256GB SSD, 2.5, SATA, 6Gbps, MLC * NVIDIA Tesla K40m * InfiniBand HCA, True Scale QLE7340, 1-port QSFP QDR memfree * dual power supply * 5-Year Warranty * 5-Year GPU Support $14,228.22 total option 2 (Tesla K80): * Dual Intel Xeon E5-2680 v3, 12C, 2.5GHz, 2133MHz RAM, 120W * 128GB, DDR4-2133 ECC, 2R (8 x 16GB) * 256GB SSD, 2.5, SATA, 6Gbps, MLC * NVIDIA Tesla K80m * InfiniBand HCA, True Scale QLE7340, 1-port QSFP QDR memfree * dual power supply * 5-Year Warranty * 5-Year GPU Support $15,524.18 total We are now running MD for systems with about 4 atoms and getting 100ns/day performance using 2 K40 GPU. Will K80 GPU act like 2 K40 as advertised in the website (http://www.gromacs.org/)? Thank you! Ruan -- 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
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] Error: 'mdrun_mpi' is not a GROMACS command.
Thanks Justin. On Tue, Aug 18, 2015 at 1:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/18/15 8:08 AM, anu chandra wrote: Dear Gromcas users, I just expericend an error while running mpi version of Gromcas on a 64 processors in a cluster. The command I used for running mdrun is as follows, mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2 But, unfortunately the run terminated with following error message. Can anyone help me to figure out what is gone wrong here? --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: 'mdrun_mpi' is not a GROMACS command. - The _mpi suffix only applies to the gmx binary, so it should be gmx_mpi mdrun ... -Justin -- == 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
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
[gmx-users] acpype problem
Hi; I want to convert amber topology and coordinate files into gromacs topology and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not found I've done the procedure mentioned in the website: https://code.google.com/p/acpype/wiki/HowToUse. I've downloaded the acpype with svn checkout http://acpype.googlecode.com/svn/trunk/ acpype command. I installed it with sudo ln -s $PWD/acpype.py /usr/local/bin/acpype command. but when I try to use acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd command, the error appeared . Thankyou, Mohammad. -- 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] Error: 'mdrun_mpi' is not a GROMACS command.
Hi, I'm using same command but without gmx_mpi and it works. On 18 Aug 2015 14:09, anu chandra anu80...@gmail.com wrote: Dear Gromcas users, I just expericend an error while running mpi version of Gromcas on a 64 processors in a cluster. The command I used for running mdrun is as follows, mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2 But, unfortunately the run terminated with following error message. Can anyone help me to figure out what is gone wrong here? --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: --- Program: gmx_mpi, VERSION 5.0.5 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 408) Function:gmx::CommandLineModuleInterface* gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*, int*, char***) Error in user input: 'mdrun_mpi' is not a GROMACS command. - Many thanks Anu -- 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] Few queries about microsecond long simulations
Many thanks for your suggestions. On Tue, Aug 18, 2015 at 12:52 PM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Hi Anu, 1) It really depends on what kind of analysis you are doing. If you are, for example, studying bio-molecular interactions that take place over microsecond long timescales then saving trajectories every 200-500 ps is advisable. I myself do receptor-membrane atomistic simulations with a saving frequency of 500 ps. You don't really need saving which is as frequent as 10 ps. 2), 3) Whereas .xtc trajectories contain only the coordinates, .trr trajectories contain both coordinates as well as velocities. So unless you are going to do any analysis which involves the velocities of atoms/particles, its safe to not write-out the .trr file. Still you are never really sure if you are going to require velocities or not and so it's best to write out the .trr file as well. On Tue, Aug 18, 2015 at 4:30 PM, Felipe Merino felipe.mer...@mpi-dortmund.mpg.de wrote: Hi, This are all questions that mostly only you can answer. On 18/08/15 12:42, anu chandra wrote: Dear Gromcas users, I am planning to do microsecond long simulation of membrane-protein system and I have ~100,000 atoms in the systems. Since I am trying for microsecond long simulations and I have a quiet large system, it can generate large amount of data and in this regard I would like to clarify few queries before continue the simulations. My queries are, 1. How often I should save the trajectories? In general, I have seen that mostly use 2ps interval for saving trajectories, as shown below. Will it be safe if I use 10ps ( 5000 steps ) interval for saving trajectories? nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps The files you create and the frequency with which you write them depends only on what you want to measure in the end. In principle, you want to save every couple of decorrelation times, for whatever property interests you. I assume that since you want a microsecond-long simulation then you are going for a slow process and therefore you don't need so frequent saving. Just as a comparison, for one of my simulations (~550k atoms, 1 µs) I save the coordinates every 40 ps which gives me a final xtc of ~50Gb of space. 2. How safe if I just write only the compressed .xtc file of the trajectories and not the .trr file during the production run? If its safe, how can I tell mdrun not to write the trr file? 3. Do I really need the trr file for any MD analysis? Again, you should know if you need the velocities later, or if need a high precision for the coordinates. If you don't, then leave the mdp as, nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 1000 nstxtcout = 1000 Many thanks in advance Anu -- 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. -- Best Regards, Ganesh Shahane -- 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] tabulated potential - problem
Hi, This is almost certainly a problem with simulation instability, so please follow the approaches here http://www.gromacs.org/Documentation/Terminology/Blowing_Up to discover more about what is wrong. Mark On Tue, Aug 18, 2015 at 3:09 PM Liz Bell lizb...@gmx.at wrote: Dear all, I have a question about the handling of the tabulated interactions. I am using tabulated potentials for my simulations. With grompp there is no problem, i.e. no error messages. Running mdrun produces: Fatal error: A tabulated bond interaction table number 1 is out of the table range: r 13.532542, between table indices 135325 and 135326, table length 6 I really do not understand this error. Considering my system it seems to be senseless. The value for r in the first column of my table is ranged from 0 to 6nm with a step size of 0.001nm. My box size is 6nm. So how is it possible that a bonded interaction is greater than the box itselfs? I am actually thinking, that it should be enough that the table is ranged from 0 to 2 or 3nm as the interaction is a bonded one. Or does this error message only occur, because of the fact that my system is crashing - so as a result from an other error in my files? Tank you very much in advance. Best, Liz -- 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
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.
