[gmx-users] Could md rerun regenerate corresponding .edr file??

[David]

On Mon, 2005-08-01 at 20:34 +0530, sunita at chem.iitb.ac.in wrote:
> Dear David,
> 
> Both nstxout and nstenergy are specified for the same number of steps
> i.e.250 and integration time is 2 fs. Lets not worry about this.
> 
> I performed md rerun in the following way.
> 
> mdrun -v -s old.tpr -rerun old.trr -e new.edr -o -c -g
> 
> Is this the correct procedure?
yes

> 
> I have calculated the kinetic energy, potential energy and temperature of
> the system from the new.edr file and compare these values with the
> corresponding files generated from existing old.edr file. There is a big
> differences in kinetic energy and temperature. Instead of 300 K
> temperature, I am getting 2.8 K. Similarly there is a large difference in
> kinetic energy. But the potential energy is coming exactly same.
> 
> Is it because the new.edr file loosing the velocity term?
> 
> If I want the exact values of temerature and kinetic energy which
> procedure I should follow to get the new.edr file and how?
I'm not sure that it is possible, because you need velocities from more
than one time step. Potential energy should be fine though.

> 
> Thanks for your response and appreciation.
> Best regards,
> sunita
> 
> > On Mon, 2005-08-01 at 11:11 +0530, sunita at chem.iitb.ac.in wrote:
> >> Dear users,
> >>
> >> I was extending a simulation. By some reasons it crashed. These
> >> simulations are performed in gromacs version 3.1.4. When I analysed the
> >> files such as .trr, .tpr and .edr files, I found the number of frames in
> >> .trr and .edr files are different. The energy file generated from the
> >> .edr
> >> file have 50 less time frames than the corresponding .trr file. I have
> >> extended many crashed simulations but have never came across such
> >> situation, in these cases both the files have same number of frames. I
> >> am
> >> saving a frame in every 0.5 ps.
> > This is not weird, you have probably specified different nstxout and
> > nstenergy
> >>
> >> In such situation can I regenerate .edr file from the corresponding .trr
> >> and .tpr file by doing md rerun?
> > yes, but do set nstenergy correctly
> >
> >
> >>
> >> Thanks for your appreciation.
> >> Sunita
> >> _______________________________________________
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> > --
> > 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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> 
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-- 
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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