Re: [gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?
In addition to others' suggestions, you also have the option of writing / converting to .gro, which already has flexible precision for the coordinate fields. Use the -prec output option if needed. Mark On Mar 18, 2014 12:00 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/17/14, 6:45 PM, Andrew DeYoung wrote: Hi Tsjerk, Thanks so much for your time. Unfortunately, when I tried to convert a .g96 configuration to a .trr trajectory, with this command: trjconv -f conf1.g96 -o conf1.trr I get this error message: --- Program trjconv_d, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am running Gromacs 4.5.5. Do you know if there is another way to convert a .g96 configuration to a .trr trajectory, without using trjconv? Or do you know if a different version of Gromacs would not have this problem? Anything in the 4.6 series or newer should work. The reading of .g96 was disabled in 2011 when there were problems, but then reinstated in late 2012, before the release of the first 4.6 beta release. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
[gmx-users] How can I concatenate multiple g96 configurations into a single trajectory?
Hi, I have been creating several .g96 configuration files by hand (actually, using a scripting language). I like .g96 as a configuration file format because it provides 9 decimal places of precision for the x, y, and z coordinates of the position and velocity of atoms in my system -- whereas .gro and .pdb configuration file formats offer much lower precision. My system is crystalline, and I found many months ago that the lower precision offered by .gro and .pdb is not quite enough to achieve the exact bond lengths that I want in my crystal. Many months ago, Professor van der Spoel suggested on this list that I switch to .g96 for my configurations. So for many months I have been successfully using .g96 configurations as input to grompp to make the .tpr files necessary for simulation. Today, however, I am trying to do something somewhat unusual, and I run into an unusual problem. Suppose I have made three .g96 configurations by hand: conf1.g96, conf2.g96, and conf3.g96. I want to compute the single-point energy of all three configurations. (Why would I want to do this? I have written code in a scripting language to generate frames in which a particular angle is scanned from one extreme to the other; I want to use Gromacs to simply compute the single-point energy at each frame in the scan, without taking any MD moves.) One way to do this might be to run three different zero-step MD simulations, by passing the three configurations separately to grompp, obtaining three separate .tpr files, and passing those three .tpr files to mdrun. But this documentation page http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy warns that zero-step MD simulations have complications related to catering to possible restarts and is not recommended. Doing it that way is also a little inconvenient because eventually I will have dozens or hundreds of separate handmade .g96 configurations for which to calculate the single-point energy, and running hundreds of zero-step simulations would probably require some sort of bash script. So, my thought is to concatenate the three (or more) .g96 configurations into a single trajectory, and then feed that trajectory to the -rerun switch of mdrun to compute the energy of each frame. My question is, how can I concatenate three (or more) .g96 configurations into a single trajectory of any type? I have tried: trjcat -f conf1.g96 conf2.g96 conf3.g96 -o output.trr But I get this error message: --- Program trjcat, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Reading trajectories in .g96 format may be broken, but reading CONFIGURATIONS in .g96 is not broken, as far as I know (I routinely pass g96 configurations to the -c switch of grompp). Is there any other way I can concatenate three (or more) .g96 configurations into a single trajectory of any type (.trr, .xtc, etc) -- WITHOUT going through .gro or .pdb (e.g., by converting from .g96 using editconf), which have lower precision? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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] How can I concatenate multiple g96 configurations into a single trajectory?
Hi Andrew, You can convert each frame to trr and concatenate those. Cheers, Tsjerk On Mar 17, 2014 8:18 PM, Andrew DeYoung adeyo...@andrew.cmu.edu wrote: Hi, I have been creating several .g96 configuration files by hand (actually, using a scripting language). I like .g96 as a configuration file format because it provides 9 decimal places of precision for the x, y, and z coordinates of the position and velocity of atoms in my system -- whereas .gro and .pdb configuration file formats offer much lower precision. My system is crystalline, and I found many months ago that the lower precision offered by .gro and .pdb is not quite enough to achieve the exact bond lengths that I want in my crystal. Many months ago, Professor van der Spoel suggested on this list that I switch to .g96 for my configurations. So for many months I have been successfully using .g96 configurations as input to grompp to make the .tpr files necessary for simulation. Today, however, I am trying to do something somewhat unusual, and I run into an unusual problem. Suppose I have made three .g96 configurations by hand: conf1.g96, conf2.g96, and conf3.g96. I want to compute the single-point energy of all three configurations. (Why would I want to do this? I have written code in a scripting language to generate frames in which a particular angle is scanned from one extreme to the other; I want to use Gromacs to simply compute the single-point energy at each frame in the scan, without taking any MD moves.) One way to do this might be to run three different zero-step MD simulations, by passing the three configurations separately to grompp, obtaining three separate .tpr files, and passing those three .tpr files to mdrun. But this documentation page http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy warns that zero-step MD simulations have complications related to catering to possible restarts and is not recommended. Doing it that way is also a little inconvenient because eventually I will have dozens or hundreds of separate handmade .g96 configurations for which to calculate the single-point energy, and running hundreds of zero-step simulations would probably require some sort of bash script. So, my thought is to concatenate the three (or more) .g96 configurations into a single trajectory, and then feed that trajectory to the -rerun switch of mdrun to compute the energy of each frame. My question is, how can I concatenate three (or more) .g96 configurations into a single trajectory of any type? I have tried: trjcat -f conf1.g96 conf2.g96 conf3.g96 -o output.trr But I get this error message: --- Program trjcat, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Reading trajectories in .g96 format may be broken, but reading CONFIGURATIONS in .g96 is not broken, as far as I know (I routinely pass g96 configurations to the -c switch of grompp). Is there any other way I can concatenate three (or more) .g96 configurations into a single trajectory of any type (.trr, .xtc, etc) -- WITHOUT going through .gro or .pdb (e.g., by converting from .g96 using editconf), which have lower precision? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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] How can I concatenate multiple g96 configurations into a single trajectory?
Hi Tsjerk, Thanks so much for your time. Unfortunately, when I tried to convert a .g96 configuration to a .trr trajectory, with this command: trjconv -f conf1.g96 -o conf1.trr I get this error message: --- Program trjconv_d, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am running Gromacs 4.5.5. Do you know if there is another way to convert a .g96 configuration to a .trr trajectory, without using trjconv? Or do you know if a different version of Gromacs would not have this problem? Thanks for your time. Andrew DeYoung Carnegie Mellon University -- 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] How can I concatenate multiple g96 configurations into a single trajectory?
On 3/17/14, 6:45 PM, Andrew DeYoung wrote: Hi Tsjerk, Thanks so much for your time. Unfortunately, when I tried to convert a .g96 configuration to a .trr trajectory, with this command: trjconv -f conf1.g96 -o conf1.trr I get this error message: --- Program trjconv_d, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am running Gromacs 4.5.5. Do you know if there is another way to convert a .g96 configuration to a .trr trajectory, without using trjconv? Or do you know if a different version of Gromacs would not have this problem? Anything in the 4.6 series or newer should work. The reading of .g96 was disabled in 2011 when there were problems, but then reinstated in late 2012, before the release of the first 4.6 beta release. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
