[gmx-users] why the values is not equal!

[chiloo Laohpongspaisan]

Dear all,

 

I've run MD 500,000 steps (1000 ps). After the job ceased, i took the last configuration of structure (file:  structure.gro), and ran MD more with the same input file. But i don't understand that why the properties of the last step of first MD is not equal to the zeroth step of the second MD. Below is the MD results of 1st MD and 2nd MD, respectively. And my MD paramerter file is as follow.

 

Best regards

Chiloo

--------------------------------------------------------

       Step           Time         Lambda      Annealing

         500000     1000.00006        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS

       Before LINCS         0.067623    241    242   0.003032

        After LINCS         0.000132    632    635   0.000012

   Energies (kJ/mol)

          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14

    1.07364e+04    2.52571e+03    4.13630e+03    7.58160e+02    3.73031e+03

     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential

    1.98057e+04    6.58396e+02   -2.04387e+05   -1.00879e+05   -2.62915e+05

    Kinetic En.   Total Energy    Temperature Pressure (bar)

    4.09683e+04   -2.21947e+05    3.10246e+02    1.66980e+02

-----------------------------------------------------------------        

   Step           Time         Lambda      Annealing

              0        0.00000        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS

       Before LINCS         0.067893    241    242   0.003031

        After LINCS         0.000118    632    635   0.000011

   Energies (kJ/mol)

          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14

    1.07468e+04    2.52814e+03    4.13693e+03    7.53671e+02    3.72928e+03

     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential

    1.98088e+04    6.62636e+02   -2.04375e+05   -1.00878e+05   -2.62887e+05

    Kinetic En.   Total Energy    Temperature Pressure (bar)

    4.09659e+04   -2.21921e+05    3.10227e+02    2.53964e+02

           Step           Time         Lambda      Annealing

              1        0.00200        0.00000        1.00000

-----------------------------------------

title               = M2 in dmPC
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  500000   ; total 1000 ps = 1 ns !
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.2
coulombtype         =  PME
rcoulomb            =  1.2
rvdw                =  1.2
pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  DMPC  SOL  Na
tau_t               =  0.1      0.1   0.1  0.1
ref_t               =  310      310   310  310
; Energy monitoring
energygrps          =  Protein  DMPC  SOL  Na
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  310.0



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