molecular dynamics output file

Clicked A Few Times

6:32:46 AM PST - Tue, Dec 4th 2012

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!!

Clicked A Few Times

11:20:56 AM PST - Tue, Dec 4th 2012
The pressure can certainly be negative, in particular at the start of an MD simulation of a non-equilibrated system. This indicates that the system is contracting. Once equilibrated, the instantaneous pressure can still be negative, but the average over time should converge to the value of the external pressure as set in the input. The statistics of properties are printed on the output file for the last 'nstat' MD steps as well as for the entire simulation. These are the two sets of three columns you see. Obviously the very first time that this block is written, the two sets are identical because the entire simulation has only progressed 'nstat' steps. Continue the simulation for a resonable simulation time and both issues should be resolved.

Clicked A Few Times

9:50:56 PM PDT - Mon, Apr 14th 2014
Hi I have tried to run MD ( Tio2 example). For this work which I need .rst and .top files, generated by Prepare Task. For Prepare Task ,we should specify 6 files.(Tio2.nw ,Tio2.pdb ,Tio2.frg ,Tio2.seq,Tio.sgm ,amber.par ). After running Prepare Task, I have .rst and .top files. Then I have tried to run the MD task (for example dynamics) but I encountered with the following error: EOF encountered on topology files I appreciate any comment. Thanks.

Clicked A Few Times

4:40:44 AM PDT - Mon, Apr 8th 2019

Hello

Quote:username

Sacch

I have got a similar issue, but in my case, the pressure never changes and is 0. I do not undertstand why I don't get any value for the pressure. Here is my input, which is basic:

echo
start lpxrlps

memory 3750 mb

permanent_dir ./perm
scratch_dir ./data

charge -2

prepare
system lpxrlps
source qmmm_opt.pdb
new_top new_seq
new_rst
amber
update lists
ignore
crop
vacuo
cube
write lpxrlps_final.pdb
write lpxrlps_final.rst
end

task prepare

basis "ao basis"
* library "6-311++G(2d,2p)"
end

dft
xc becke88 lyp
disp vdw 2
end

md
system lpxrlps_final
noshake solute
cutoff 1.0
isotherm 0.0 50.0 anneal 0 10
isobar anisotropic
equil 0 data 100000
record rest 1000 prop 200
print step 1000 energies 1000 timing
mwm 3000
msa 3000
end

qmmm
#bq_zone 3.0
link_atoms hydrogen
region mm
density espfit
print low
end

task qmmm dft dynamics

And I get the following output:

                                           Statistics over last      100 steps     Statistics over last    61600 steps
                                           Average     RMS fluct     Drift/ps      Average     RMS fluct     Drift/ps

 Step                                    6.15505E+04  2.88661E+01  1.00000E+03   3.08005E+04  1.77824E+04  1.00000E+03
 Time                                    6.15505E+01  2.88661E-02  1.00000E+00   3.08005E+01  1.77824E+01  1.00000E+00           ps
 Number solvent-solvent interactions SR  9.44285E+05  6.79407E+01 -1.22618E+03   9.43829E+05  5.82342E+03  5.11688E+01
 Number solvent-solute interactions  SR  2.91579E+04  1.20255E+01  1.09931E+01   2.89228E+04  8.41704E+02  2.22679E+01
 Number solute-solute interactions   SR  1.78885E+06  1.10976E+03 -1.23716E+04   1.78624E+06  1.21936E+04  1.34994E+02
 Number of solvent SHAKE iterations      2.30000E+01  0.00000E+00  0.00000E+00   2.30000E+01  0.00000E+00  3.82498E-16
 Number of solute SHAKE iterations       1.00000E+00  0.00000E+00 -1.09150E-11   1.00000E+00  0.00000E+00  0.00000E+00
 Volume                                  5.60837E+02  1.50344E-03 -5.20821E-02   5.62441E+02  9.28793E-01 -5.22311E-02        nm**3
 Mass density                            9.20578E+02  2.46760E-03  8.54894E-02   9.17954E+02  1.51587E+00  8.52458E-02      kg/m**3
 Pressure                                0.00000E+00  0.00000E+00  0.00000E+00   0.00000E+00  0.00000E+00  0.00000E+00           Pa
 Pressure scaling                        1.00000E+00  3.57628E-08 -1.63725E-10   1.00000E+00  1.56780E-06 -4.82665E-14
 Temperature                             5.03375E+01  1.28869E-01 -1.42488E+00   4.62561E+01  1.08188E+01  3.52932E-01            K
 Temperature solvent                     5.24141E+01  1.38994E-01 -1.95468E+00   4.88033E+01  1.12929E+01  3.44754E-01            K
 Temperature solute                      3.72563E+01  3.36141E-01  1.91261E+00   3.02097E+01  8.61108E+00  4.04446E-01            K
 Temperature scaling solvent             9.99966E-01  1.26510E-05  1.29683E-04   9.99922E-01  3.99625E-04  4.45769E-06
 Temperature scaling solute              9.99966E-01  1.26510E-05  1.29683E-04   9.99922E-01  3.99625E-04  4.45769E-06
 Energy electrostatic                   -1.02116E+06  3.81401E+02 -1.10617E+04  -1.01961E+06  4.20661E+03 -8.21697E+01       kJ/mol
 Energy van der Waals                    1.90480E+05  2.45723E+02  8.36219E+03   1.90385E+05  2.56083E+03  2.39515E+01       kJ/mol
 Energy potential                       -8.15392E+05  2.16132E+02 -2.87961E+03  -8.14368E+05  1.77274E+03 -3.51628E+01       kJ/mol
 Energy kinetic                          2.23035E+04  5.70990E+01 -6.31336E+02   2.04951E+04  4.79358E+03  1.56377E+02       kJ/mol
 Energy total                           -7.93088E+05  1.98145E+02 -3.51095E+03  -7.93873E+05  5.19209E+03  1.21214E+02       kJ/mol

with no pressure...

Any idea please ?

Thanks,
Bastien

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