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!!
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