Antw: Re: Antw: [gmx-users] tpbconv for following runs

[Peter Friedel]

high, alan,
ester did write, that the difference was between the last step of run1 and first step of run2. I cannot find any leap frog step between.
cheers, peter

<<< Alan Wilter Sousa da Silva <alan at biof.ufrj.br> 10.03. 13.33 >>>
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
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>

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

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.