molecular dynamics output file


Click here for full thread
Clicked A Few Times
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