[gmx-users] rerun queries

[David]

On Wed, 2005-06-15 at 12:30 +0530, Dilraj Lama wrote:

> Actual run:
> ***********
>  Energies (kJ/mol)
>         G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
>     1.66276e+02    7.68902e+02    1.56747e+03    3.56898e+02    9.03171e+02
>      Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
>     2.06463e+04    1.73125e+05   -2.99305e+03   -1.04107e+06   -7.97644e+02
>  Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
>     1.34345e-02   -8.47326e+05    1.30418e+05   -7.16908e+05    3.00277e+02
>  Pressure (bar)
>     8.54693e+02
> 
> Rerun run:
> **********
>  Energies (kJ/mol)
>         G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
>     1.66276e+02    7.68902e+02    1.56747e+03    3.56898e+02    9.03180e+02
>      Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
>     2.06465e+04    1.73125e+05   -2.99305e+03   -1.04107e+06   -7.97597e+02
>  Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
>     2.40138e-04   -8.47325e+05    1.30418e+05   -7.16908e+05    3.00277e+02
>  Pressure (bar)
>     8.55262e+02
> 
> The energy values for all terms are identical except for "Position Rest." , "Temperature" ,
> *****************************************************************************************
> "Pressure" and hence for "Potential" and "Total Energy".
> ********************************************************
> 
> Are Differences in "TEMPERATURE" and hence for "KINETIC ENERGY" and also for "PRESSURE" arising
> because i am not saving the velocities in the actual ".trr" at every step at which i am saving the
> coordinates as mentioned in the WARNING message ????????
Indeed, temperature will not be correct, but you're not interested in
that probably. Position restraint is a bit strange although the
differences are small. Try
gmxcheck -s1 top -s2 top
to see whether there are any other differences in your tpr files.

You may also want to check the definitions of your posres. Do they act
only on the peptide maybe?
> 

-- 
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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