Hi. I get two different volumes with g_energy and gmxdump.
Which one is true? For now, I'm trying to get a NVT simulation with correct pressure, after a 300 ns NPT equilibration. The 400 ns NPT equilibration has the following statistics, according to g_energy of gromacs 4.6.7, and the equilibration seems to be sufficient. Last energy frame read 21438168 time 428763.375 Statistics over 214381681 steps [ 0.0000 through 428763.3600 ps ], 5 data sets All statistics are over 17108015 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Total Energy -307350 6.1 nan -15.4944 (kJ/mol) Temperature 299.851 0.0018 nan -0.00756116 (K) Pressure 1.01127 5.7e-05 nan 0.000126851 (bar) Volume 298.385 0.0043 nan 0.00672558 (nm^3) Density 1015.42 0.015 nan -0.0229017 (kg/m^3) gcq#328: "I used to be blond and stupid, but now I dyed it black" (Miss Li) The nan in RMSD is caused by that I did one restart of the simulation. Getting the correct volume is very important for me because the isothermal compressibility of water is 4.5e-5, and a small change in volume can lead to a relatively large change in pressure. gromacs5.0.1. g_energy_d time(ps) box-x box-y box-z volume ------------- -------- -------- -------- ---------- 125142.100000 7.500611 7.500611 5.303739 298.383881 gromacs4.6.7. g_energy time(ps) volume ------------- ---------- 125142.100000 298.383881 gromacs4.6.7. gmxdump box (3x3): box[ 0]={ 7.50577e+00, 0.00000e+00, 0.00000e+00} box[ 1]={ 0.00000e+00, 7.50577e+00, 0.00000e+00} box[ 2]={ 3.75289e+00, 3.75289e+00, 5.30739e+00} from the box vectors, volume is |z dot (x cross y)| 7.50577 * 7.50577 * 5.30739 = 299.000218803 gromacs5.0.1. gmxdump_d box (3x3): box[ 0]={ 7.50577e+00, 0.00000e+00, 0.00000e+00} box[ 1]={ 0.00000e+00, 7.50577e+00, 0.00000e+00} box[ 2]={ 3.75289e+00, 3.75289e+00, 5.30739e+00} example command for running gmx_dump: gmxdump_d -s ../npt13c.tpr -f ../npt13c_step62571050.cpt &> gmxdump5.0.1d_step62571050 example command for running g_energy: g_energy_d -f ../npt13c.edr npt13c_volume_gromacs5.0.1_d.xvg since the timestep is 0.002 ps, the time(ps) corresponding to the check point file is: 62571050 * 0.002 = 125142.1 ps All the files (tpr, cpt, edr) are generated by mdrun of gromacs4.6.7 (mixed precision). It seems that it is ok to use the g_energy and gmxdump of gromacs 5.0.1 on these files. Size of the .edr file is 5 gb. Thank you again. -- 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.