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

[David van der Spoel]

On Wed, 2005-08-03 at 03:30 -0700, chiloo Laohpongspaisan wrote:
> 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.
use tpbconv to continue simulations.
> 
>  
> 
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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