Antw: [gmx-users] tpbconv for following runs

[Peter Friedel]

hi, ester,
i think, you can be quiet at all.
i compared all individual energies , and i found, that there is only a small difference in kinetic energies, which influences the total energy, the temperature and also the pressure directly. because the velocities may be initialized new at the beginning of every run from the maxwell distribution, in my oppinion it doesn't matter.
cheers, peter

<<< Ester Chiessi <ester.chiessi at uniroma2.it> 10.03. 09.52 >>>
Hi all,

I'm using tpbconv to produce an MD calculation by following runs.

To syntax is:

tpbconv -s run1.tpr -f run1.trr -extend 1.0 -o run2



Gromacs:   VERSION 3.1.4 (double precision)

I have a cubic box (l=4.272 nm) of water SPC containing a linear polymer.
There are 2381 molecules, 2596 charge groups and 7564 atoms


This is at the last step of run1:

           Step           Time         Lambda      Annealing
           1000        1.00000        0.00000        1.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
    4.92527e+02    9.06575e+02    7.93562e+02    1.01232e+02    6.11300e+01
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential
   -7.30751e+03    1.52176e+04   -1.08284e+05   -3.44624e+03   -1.01465e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    1.94824e+04   -8.19828e+04    3.03304e+02    5.93431e+01


This is at the first step of run2:
......
bUncStart            = TRUE
......

           Step           Time         Lambda      Annealing
              0        1.00000        0.00000        1.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
    4.92527e+02    9.06575e+02    7.93562e+02    1.01232e+02    6.11300e+01
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential
   -7.30751e+03    1.52176e+04   -1.08284e+05   -3.44624e+03   -1.01465e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    1.94640e+04   -8.20011e+04    3.03019e+02    7.98155e+01

I expected that all terms were identical, not only the potential energy
contributions.

May I consider negligible these discrepances?

Thanks

Ester

--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328


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