[gmx-users] tpbconv for following runs

[Ester Chiessi]

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