Antw: [gmx-users] tpbconv for following runs

[Alan Wilter Sousa da Silva]

Hi List!

IMHO, I think that you have such a difference in velocities (and so on)
because of Leap frog algorithm, in which position and velocities are
calculated in half time step alternately.  So I found out it normal.

Cheers

On Mon, 10 Mar 2003, Peter Friedel wrote:

> 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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-- 
-----------------------
Alan Wilter S. da Silva
-----------------------
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil