Thank you so much for all of your help,
Jason, you were right, I was running my simulations on an amber
installation that wasn't the one I was editing. (echo $AMBERHOME is now
going to live in all of my scripts) after solving some (smaller) issues I
was able to get
Etot = -5080668.3730 EKtot = 0.0000 EPtot =
-5080668.3730
Etot = -5080668.3730 EKtot = 0.0000
EPtot = -5080668.3730
In my mdout file!
Thanks again for all of the help!
John
On Wed, Jul 1, 2015 at 12:00 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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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>
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Received on Thu Jul 02 2015 - 10:30:03 PDT
