On Wed, 2015-07-01 at 08:38 -0400, David A Case wrote:
> 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?
It seemed to me that the original simulation was a set of free ions that
were associating by electrostatic interactions (the mdout *also* had
only nonbonded interactions). With rigid water and a large number of
closely-associating free ions as the only particles, this is about what
I'd expect. The T_solv looks weird, but perhaps that's because Amber
doesn't really discern "solvent" and "solute" differences as strictly as
it used to?
But if there *are* flexible bonds in the system, then this is indeed
strange output.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 01 2015 - 09:30:03 PDT
