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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Received on Tue Jun 30 2015 - 12:00:02 PDT
