On Tue, Jun 30, 2015, John Dood wrote:
>
> 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.
The above is indeed odd. Do the numbers for the vdw and electrostatic
energies match those in the mdout file? Do you perhaps actually have no bonds
or angles in your simulation? Are you using the patched or unpatched version
of dynlib?
...dac
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Received on Wed Jul 01 2015 - 06:00:03 PDT
