molecular dynamics output file


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Dear all

I am a bit confused about the output file I generated. The test run of my system is composed of a peptide solvated inside a box with periodic boundary. First I minimise the solvent, then I minimize the solute. Then I run a dynamics (oops I ran an additional optimisation?!). The script is the following:

echo
start MT2
memory total 1000 mb

prepare
read MT2_ref.rst
write MT2_fslu.rst
end
task prepare

md
system MT2_fslu
fix solute
sd 100
end

task md optimize

task shell "cp MT2_fslu.qrs MT2_fsol.rst"

md
system MT2_fsol
fix solvent
sd 100
end

task md optimize

task shell "cp MT2_fsol.qrs MT2_dyn.rst"

md
system MT2_dyn
noshake solute
isotherm 0 298.15 anneal 0 3
isobar
cutoff 1.0
data 50000 step 0.001
print step 1000 stat 1000 forces 1000 energies 1000
record rest 1000 coord 100 times 1000 prop 1000
end

task md optimize
task md dynamics

prepare
read MT2_dyn.rst
write MT2_dyn.pdb
end



Here is the part confuses me. I plot out the "Pressure" and check the values and found that the pressure is negative on the column says "Statistics Average". I guess there is something wrong with my setting.

The second part confuses me is the header of the table. There are two of each three titles on six columns. I struggled to search on Google and on this forum to find out if there'd been anyone discussed about this but I cannot find any. Could someone please give me a hint?


 MOLECULAR DYNAMICS STATISTICAL INFORMATION                                                                  12/04/12   17:50:41

                                           Statistics over last     1000 steps     Statistics over last     1000 steps
                                           Average     RMS fluct     Drift/ps      Average     RMS fluct     Drift/ps

 
 Step                                    5.00500E+02  2.88675E+02  1.00000E+03   5.00500E+02  2.88675E+02  1.00000E+03
 Time                                    5.00500E-01  2.88675E-01  1.00000E+00   5.00500E-01  2.88675E-01  1.00000E+00           ps
 Number solvent-solvent interactions SR  4.93866E+05  7.81740E+03  2.36933E+04   4.93866E+05  7.81740E+03  2.36933E+04
 Number solvent-solute interactions  SR  8.88155E+03  4.88191E+02  1.64501E+03   8.88155E+03  4.88191E+02  1.64501E+03
 Number solute-solute interactions   SR  2.03779E+05  1.73219E+03  9.68458E+02   2.03779E+05  1.73219E+03  9.68458E+02
 Number of solvent SHAKE iterations      2.30000E+01  0.00000E+00 -2.18279E-14   2.30000E+01  0.00000E+00 -2.18279E-14
 Number of solute SHAKE iterations       1.00000E+00  0.00000E+00 -6.82122E-16   1.00000E+00  0.00000E+00 -6.82122E-16
 Volume                                  2.03871E+02  3.56483E+00 -1.11069E+01   2.03871E+02  3.56483E+00 -1.11069E+01        nm**3
 Mass density                            1.06517E+03  1.82249E+01  5.71974E+01   1.06517E+03  1.82249E+01  5.71974E+01      kg/m**3
 Pressure                               -8.04343E+07  1.07936E+08  2.83617E+08  -8.04343E+07  1.07936E+08  2.83617E+08           Pa
 Pressure scaling                        9.99927E-01  9.77896E-05  2.56957E-04   9.99927E-01  9.77896E-05  2.56957E-04
 Temperature                             4.82946E+01  1.75438E+01  5.79852E+01   4.82946E+01  1.75438E+01  5.79852E+01            K
 Temperature solvent                     4.90997E+01  1.80223E+01  5.95794E+01   4.90997E+01  1.80223E+01  5.95794E+01            K
 Temperature solute                      3.67684E+01  1.08442E+01  3.51646E+01   3.67684E+01  1.08442E+01  3.51646E+01            K
 Temperature scaling solvent             9.99795E-01  2.75376E-03  4.57033E-03   9.99795E-01  2.75376E-03  4.57033E-03
 Temperature scaling solute              9.99795E-01  2.75376E-03  4.57033E-03   9.99795E-01  2.75376E-03  4.57033E-03
 Energy electrostatic                   -4.34141E+05  7.76123E+03 -1.39255E+04  -4.34141E+05  7.76123E+03 -1.39255E+04       kJ/mol
 Energy van der Waals                    8.14109E+04  4.05171E+03  7.54657E+03   8.14109E+04  4.05171E+03  7.54657E+03       kJ/mol
 Energy potential                       -3.49465E+05  3.78846E+03 -6.10115E+03  -3.49465E+05  3.78846E+03 -6.10115E+03       kJ/mol
 Energy kinetic                          8.84614E+03  3.21351E+03  1.06212E+04   8.84614E+03  3.21351E+03  1.06212E+04       kJ/mol
 Energy total                           -3.40618E+05  3.72557E+03  4.52004E+03  -3.40618E+05  3.72557E+03  4.52004E+03       kJ/mol
 Energy solvent intra electrostatic      3.58301E+04  7.89024E-03  5.49853E-09   3.58301E+04  7.89024E-03  5.49853E-09       kJ/mol
 Energy solvent intra van der Waals      0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solvent inter electrostatic     -4.55800E+05  6.86661E+03 -1.05106E+04  -4.55800E+05  6.86661E+03 -1.05106E+04       kJ/mol
 Energy solvent inter van der Waals      8.29628E+04  3.98280E+03  7.34772E+03   8.29628E+04  3.98280E+03  7.34772E+03       kJ/mol
 Energy solvent bonds                    0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solvent Urey-Bradley             0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solvent proper dihedrals         0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solvent improper dihedrals       0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solvent polarization             0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solvent kinetic                  0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Synchronization time                    1.44031E+00  7.05709E-01  9.04293E-02   1.44031E+00  7.05709E-01  9.04293E-02            s
 Efficiency load balancing               3.94369E-01  3.35332E-02 -8.43360E-03   3.94369E-01  3.35332E-02 -8.43360E-03
 Time per step                           4.82844E-02  1.51856E-02  2.03268E-03   4.82844E-02  1.51856E-02  2.03268E-03            s
 Virial tensor element (1,1)             1.73639E+04  1.30399E+04 -3.40362E+04   1.73639E+04  1.30399E+04 -3.40362E+04       kJ/mol
 Virial tensor element (1,2)            -1.82616E+01  1.60954E+03 -7.20103E+02  -1.82616E+01  1.60954E+03 -7.20103E+02       kJ/mol
 Virial tensor element (1,3)            -3.45220E+03  1.15239E+03  9.06085E+02  -3.45220E+03  1.15239E+03  9.06085E+02       kJ/mol
 Virial tensor element (2,1)            -6.62087E+00  1.61219E+03 -1.89485E+03  -6.62087E+00  1.61219E+03 -1.89485E+03       kJ/mol
 Virial tensor element (2,2)             1.39839E+04  1.06709E+04 -2.36031E+04   1.39839E+04  1.06709E+04 -2.36031E+04       kJ/mol
 Virial tensor element (2,3)             2.24824E+03  1.94955E+03  2.65664E+03   2.24824E+03  1.94955E+03  2.65664E+03       kJ/mol
 Virial tensor element (3,1)            -3.59650E+03  1.60313E+03  8.03525E+02  -3.59650E+03  1.60313E+03  8.03525E+02       kJ/mol
 Virial tensor element (3,2)             2.25290E+03  2.25944E+03  4.35689E+03   2.25290E+03  2.25944E+03  4.35689E+03       kJ/mol
 Virial tensor element (3,3)             1.38398E+04  1.43337E+04 -3.40262E+04   1.38398E+04  1.43337E+04 -3.40262E+04       kJ/mol
 Pressure tensor element (1,1)          -3.27948E+07  3.74029E+07  1.02995E+08  -3.27948E+07  3.74029E+07  1.02995E+08           Pa
 Pressure tensor element (1,2)           8.01757E+04  4.20862E+06  1.53179E+06   8.01757E+04  4.20862E+06  1.53179E+06           Pa
 Pressure tensor element (1,3)           9.02119E+06  3.03566E+06 -1.55283E+06   9.02119E+06  3.03566E+06 -1.55283E+06           Pa
 Pressure tensor element (2,1)           6.03505E+04  4.19668E+06  4.72389E+06   6.03505E+04  4.19668E+06  4.72389E+06           Pa
 Pressure tensor element (2,2)          -2.41458E+07  3.11691E+07  7.66593E+07  -2.41458E+07  3.11691E+07  7.66593E+07           Pa
 Pressure tensor element (2,3)          -5.97343E+06  5.41601E+06 -7.93790E+06  -5.97343E+06  5.41601E+06 -7.93790E+06           Pa
 Pressure tensor element (3,1)           9.41008E+06  4.24903E+06 -1.22501E+06   9.41008E+06  4.24903E+06 -1.22501E+06           Pa
 Pressure tensor element (3,2)          -6.00369E+06  6.28751E+06 -1.25613E+07  -6.00369E+06  6.28751E+06 -1.25613E+07           Pa
 Pressure tensor element (3,3)          -2.34937E+07  4.06495E+07  1.03963E+08  -2.34937E+07  4.06495E+07  1.03963E+08           Pa
 Kinetic energy element (1,1)            2.52770E+03  8.18019E+02  2.63105E+03   2.52770E+03  8.18019E+02  2.63105E+03       kJ/mol
 Kinetic energy element (1,2)            2.23931E+00  5.15864E+01 -5.67262E+01   2.23931E+00  5.15864E+01 -5.67262E+01       kJ/mol
 Kinetic energy element (1,3)           -6.16841E+01  5.87685E+01  6.08974E+01  -6.16841E+01  5.87685E+01  6.08974E+01       kJ/mol
 Kinetic energy element (2,1)            2.23931E+00  5.15864E+01 -5.67262E+01   2.23931E+00  5.15864E+01 -5.67262E+01       kJ/mol
 Kinetic energy element (2,2)            2.45773E+03  8.61801E+02  2.84260E+03   2.45773E+03  8.61801E+02  2.84260E+03       kJ/mol
 Kinetic energy element (2,3)            3.35658E+01  4.92350E+01 -1.03346E+02   3.35658E+01  4.92350E+01 -1.03346E+02       kJ/mol
 Kinetic energy element (3,1)           -6.16841E+01  5.87685E+01  6.08974E+01  -6.16841E+01  5.87685E+01  6.08974E+01       kJ/mol
 Kinetic energy element (3,2)            3.35658E+01  4.92350E+01 -1.03346E+02   3.35658E+01  4.92350E+01 -1.03346E+02       kJ/mol
 Kinetic energy element (3,3)            2.47149E+03  8.53608E+02  2.77723E+03   2.47149E+03  8.53608E+02  2.77723E+03       kJ/mol
 Box x-dimension                         5.88533E+00  3.40547E-02 -1.06367E-01   5.88533E+00  3.40547E-02 -1.06367E-01           nm
 Box y-dimension                         5.88533E+00  3.40547E-02 -1.06367E-01   5.88533E+00  3.40547E-02 -1.06367E-01           nm
 Box z-dimension                         5.88533E+00  3.40547E-02 -1.06367E-01   5.88533E+00  3.40547E-02 -1.06367E-01           nm
 Energy solute   1 intra-electrostatic  -2.06592E+04  1.45756E+02 -1.94440E+02  -2.06592E+04  1.45756E+02 -1.94440E+02       kJ/mol
 Energy solute   1 intra-van der Waals  -1.82003E+03  3.73558E+01  9.05017E+01  -1.82003E+03  3.73558E+01  9.05017E+01       kJ/mol
 Energy solute   1-solvent electrostatic-6.29945E+03  9.61058E+02 -3.02516E+03  -6.29945E+03  9.61058E+02 -3.02516E+03       kJ/mol
 Energy solute   1-solvent van der Waals-5.65543E+02  8.91054E+01  8.47614E+01  -5.65543E+02  8.91054E+01  8.47614E+01       kJ/mol
 Energy solute   1 bonds                 1.63251E+02  1.78378E+01  4.65745E+01   1.63251E+02  1.78378E+01  4.65745E+01       kJ/mol
 Energy solute   1 angles                6.44635E+02  6.44926E+01  2.14748E+02   6.44635E+02  6.44926E+01  2.14748E+02       kJ/mol
 Energy solute   1 Urey-Bradley          0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solute   1 proper dihedrals      2.45730E+03  2.39418E+01  1.64406E+01   2.45730E+03  2.39418E+01  1.64406E+01       kJ/mol
 Energy solute   1 improper dihedrals    0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00       kJ/mol
 Energy solute   1 van der Waals 3rd     8.33666E+02  2.71230E+01  2.35904E+01   8.33666E+02  2.71230E+01  2.35904E+01       kJ/mol
 Energy solute   1 electrostatic 3rd     1.27877E+04  8.75301E+01 -1.95250E+02   1.27877E+04  8.75301E+01 -1.95250E+02       kJ/mol
 Energy solute   1 van der Waals nb     -1.82003E+03  3.73558E+01  9.05017E+01  -1.82003E+03  3.73558E+01  9.05017E+01       kJ/mol
 Energy solute   1 electrostatic nb     -2.06592E+04  1.45756E+02 -1.94440E+02  -2.06592E+04  1.45756E+02 -1.94440E+02       kJ/mol
 Energy solute   1 kinetic               4.39761E+02  1.29699E+02  4.20579E+02   4.39761E+02  1.29699E+02  4.20579E+02       kJ/mol
 Energy solute   1 potential            -9.02517E+03  5.26897E+02 -1.46803E+03  -9.02517E+03  5.26897E+02 -1.46803E+03       kJ/mol



Many thanks!!