[gmx-users] change edr file to a new origen time
Dear users, I have a dinamic that I have continued from a previous one. The problem is that I have runned in different gromacs versions, and now the results seems to be different. There's any way to set up the edr file to time 0, even now the time is another?. In order to do the same with the trr file I have used trjconv with the "-t0 0" option. How I can do that with the edr file?. I been trying -t0 option in eneconv but enven in the 3.2.1 manual seems to exist, there is not. I'm using gromacs 3.3.1. Thanks. Hector Martínez-Seara Monne University of Barcelona Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: Can't determine precision of trn file, quit!
Hello gromacs users, I ecountered the following error while performing the analysis of the MD run using the tpr and trr files. Select a group: 1Selected 1: 'Protein'trn version: GMX_trn_file (single precision)Reading frame 830 time 830.000 Fatal error: Can not determine precision of trn file, quit! The following is the md run log file extract , which shows that run there was no problem in the course of the md run:It was a 1ns md run. Step Time Lambda 414750 829.50006 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.069666 2352 2353 0.006386 After LINCS 0.82 97 100 0.22 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.93016e+03 2.17805e+03 2.04973e+03 3.94265e+03 4.00753e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.81211e+04 -4.95081e+05 -1.22241e+05 -5.05025e+05 9.15110e+04 Total Energy Temperature Pressure (bar) -4.13514e+05 3.00995e+02 5.71544e+01 Step Time Lambda 415000 830.6 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.055821 592 593 0.006322 After LINCS 0.92 737 740 0.23 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.92525e+03 2.23574e+03 2.12064e+03 3.87417e+03 4.00050e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.91018e+04 -4.95440e+05 -1.22146e+05 -5.04324e+05 9.08269e+04 Total Energy Temperature Pressure (bar) -4.13497e+05 2.98745e+02 1.00768e+02 Step Time Lambda 415250 830.50006 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.055036 2376 2377 0.006529 After LINCS 0.85 352 355 0.23 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.97620e+03 2.06364e+03 2.02333e+03 3.87432e+03 4.00435e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.84707e+04 -4.95169e+05 -1.22238e+05 -5.04956e+05 9.11952e+04 Total Energy Temperature Pressure (bar) -4.13760e+05 2.99956e+02 6.63849e+01 Step Time Lambda 415500 831.6 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.053770 796 797 0.006382 After LINCS 0.74 211 213 0.23 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.88532e+03 2.09403e+03 2.03899e+03 3.88290e+03 4.00235e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.78752e+04 -4.93795e+05 -1.22139e+05 -5.04134e+05 9.10775e+04 Total Energy Temperature Pressure (bar) -4.13057e+05 2.99569e+02 -3.85286e+01 -- -- -- Step Time Lambda 50 1000.6 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.068457 1042 1043 0.006487 After LINCS 0.87 614 618 0.22 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 6.19012e+03 2.21099e+03 2.03782e+03 3.86956e+03 3.99484e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.86097e+04 -4.94645e+05 -1.22277e+05 -5.04055e+05 9.09963e+04 Total Energy Temperature Pressure (bar) -4.13059e+05 2.99302e+02 1.08973e+02 Total NODE time on node 0: 886749Average NODE time: 443374Load imbalance reduced performance to 200% of max --- Since there is a problem in the 830ps I am not able to use the trr file for my MD analysis part.I even tried to rerun the MD from few ps before the problematic ps, but while concatenating the trr files I faced the same problem at the 830 ps of the previous trr files. Kindly please let me know, what is the real problem behind it, why it is showing such an error? What can be done to rectify the same. Also please do let me know how to assign the endtime while concatenating the 2 trr files. There is an option to mention the starting time for the respective trr files to be concatenated, but there is no option to mention the end time in the trjcat command for each trr files. If we don't specify the end time for the first trr file, then it stops with the same error : File Current start (ps) New start (ps)--
[gmx-users] Your computational box has shrunk too much!
Hello GMX-usersWhen I wanted to analysis the hbond interaction between the protein and the dppc headgroup, I got the following error:Program g_hbond, VERSION 3.3.1Source code file: gmx_hbond.c, line: 631 Fatal error:Your computational box has shrunk too much.g_hbond can not handle this situation, sorry.I found that if I set -e and -b option, for example, first I use g_hbond -e 2050, then use g_hbond -b 2050, I can get through the problem.Was there something I did wrong here? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: Can't determine precision of trn file, quit!
Hello gromacs users, I ecountered the following error while performing the analysis of the MD run using the tpr and trr files. Select a group: 1Selected 1: 'Protein'trn version: GMX_trn_file (single precision)Reading frame 830 time 830.000 Fatal error: Can not determine precision of trn file, quit! The following is the md run log file extract , which shows that run there was no problem in the course of the md run:It was a 1ns md run. Step Time Lambda 414750 829.50006 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.069666 2352 2353 0.006386 After LINCS 0.82 97 100 0.22 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.93016e+03 2.17805e+03 2.04973e+03 3.94265e+03 4.00753e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.81211e+04 -4.95081e+05 -1.22241e+05 -5.05025e+05 9.15110e+04 Total Energy Temperature Pressure (bar) -4.13514e+05 3.00995e+02 5.71544e+01 Step Time Lambda 415000 830.6 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.055821 592 593 0.006322 After LINCS 0.92 737 740 0.23 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.92525e+03 2.23574e+03 2.12064e+03 3.87417e+03 4.00050e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.91018e+04 -4.95440e+05 -1.22146e+05 -5.04324e+05 9.08269e+04 Total Energy Temperature Pressure (bar) -4.13497e+05 2.98745e+02 1.00768e+02 Step Time Lambda 415250 830.50006 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.055036 2376 2377 0.006529 After LINCS 0.85 352 355 0.23 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.97620e+03 2.06364e+03 2.02333e+03 3.87432e+03 4.00435e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.84707e+04 -4.95169e+05 -1.22238e+05 -5.04956e+05 9.11952e+04 Total Energy Temperature Pressure (bar) -4.13760e+05 2.99956e+02 6.63849e+01 Step Time Lambda 415500 831.6 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.053770 796 797 0.006382 After LINCS 0.74 211 213 0.23 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 5.88532e+03 2.09403e+03 2.03899e+03 3.88290e+03 4.00235e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.78752e+04 -4.93795e+05 -1.22139e+05 -5.04134e+05 9.10775e+04 Total Energy Temperature Pressure (bar) -4.13057e+05 2.99569e+02 -3.85286e+01 -- -- -- Step Time Lambda 50 1000.6 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.068457 1042 1043 0.006487 After LINCS 0.87 614 618 0.22 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 6.19012e+03 2.21099e+03 2.03782e+03 3.86956e+03 3.99484e+04 LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En. 5.86097e+04 -4.94645e+05 -1.22277e+05 -5.04055e+05 9.09963e+04 Total Energy Temperature Pressure (bar) -4.13059e+05 2.99302e+02 1.08973e+02 Total NODE time on node 0: 886749Average NODE time: 443374Load imbalance reduced performance to 200% of max --- Since there is a problem in the 830ps I am not able to use the trr file for my MD analysis part.I even tried to rerun the MD from few ps before the problematic ps, but while concatenating the trr files I faced the same problem at the 830 ps of the previous trr files. Kindly please let me know, what is the real problem behind it, why it is showing such an error? What can be done to rectify the same. Also please do let me know how to assign the endtime while concatenating the 2 trr files. There is an option to mention the starting time for the respective trr files to be concatenated, but there is no option to mention the end time in the trjcat command for each trr files. If we don't specify the end time for the first trr file, then it stops with the same error : File Current start (ps) New start (ps)
