And to add to this...
If one looks at the format statements that go along with the code John
showed in his original email, it seems clear to me that these statements in
the dynlib.F90 do not represent what is in the mden file.
But maybe it is easier to come back to his original question. If one
wanted to modify the format of the mdout file. Where is the code that
actually writes this?
Thanks,
Brent
On Tue, Jun 30, 2015 at 2:38 PM, John Dood <john.dood.hope.edu> wrote:
> Thank you Professor Case,
>
> I enabled the writing to the mden file and specified the file name in the
> command line arguments. After running the simulation I found that the mden
> file contained:
>
> L0 Nsteps time(ps) Etot EKinetic
> L1 Temp T_solute T_solv Pres_scal_solu
> L2 Pres_scal_solv BoxX BoxY BoxZ
> L3 volume pres_X pres_Y pres_Z
> L4 Pressure EKCoM_x EKCoM_y EKCoM_z
> L5 EKComTot VIRIAL_x VIRIAL_y VIRIAL_z
> L6 VIRIAL_tot E_pot E_vdw E_el
> L7 E_hbon E_bon E_angle E_dih
> L8 E_14vdw E_14el E_const E_pol
> L9 AV_permMoment AV_indMoment AV_totMoment Density
> dV/dlambda
> L0 1 0.2000000000E-02 -.5080668373E+07 0.3720109068E-29
> L1 0.1950075675E-31 0.1950075675E-31 -.5080668414E+13 0.1000000000E+01
> L2 0.1000000000E+01 0.1006400000E+03 0.1006400000E+03 0.1006400000E+03
> L3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> L4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> L5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> L6 0.0000000000E+00 -.5080668373E+07 0.2318587581E+07 -.7399255954E+07
> L7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> L8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> L9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> 0.0000000000E+00
>
> Having looked through the code I wrote, and the code around it, I am still
> confused because this output does not look at all like what I would expect.
> I think I am still in need of additional help.
>
> Thanks,
>
> John
>
> On Tue, Jun 30, 2015 at 2:00 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Tue, Jun 30, 2015, John Dood wrote:
> >
> > > I have tried modifying
> > > $AMBERHOME/AmberTools/src/sander/dynlib.F90 in two different ways and I
> > am
> > > not seeing any change in either the mdout file or the mdinfo file.
> >
> > That is correct: this code writes to the mden file, specified by the -e
> > flag on
> > the sander command line.
> >
> > ....dac
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Tue Jun 30 2015 - 22:00:03 PDT
