Thanks Jason,
Best,
Hirdesh
On Tue, Oct 4, 2016 at 3:21 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Oct 4, 2016 at 8:48 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
>
> > Hi,
> > I am doing a long simulation of my protein-ligand complex. In the out
> file,
> > the time step was written as:
> > TIME(PS) = 335980.000 (note XXX.000 format)..
> >
> >
> > NSTEP =139790000 *TIME(PS) = 335980.000* TEMP(K) = 298.18 PRESS
> > = 15.6
> > Etot = -115980.9003 EKtot = 27977.8633 EPtot =
> > -143958.7636
> > BOND = 1085.4143 ANGLE = 2911.4185 DIHED =
> > 4565.4169
> > 1-4 NB = 1346.0456 1-4 EEL = 14330.8565 VDWAALS =
> > 16001.0010
> > EELEC = -184198.9163 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 12017.9146 VIRIAL = 11864.6655 VOLUME =
> > 455008.3585
> > Density =
> > 1.0337
> > ------------------------------------------------------------
> > ------------------
> >
> > wrapping first mol.: -27.96280 -39.54537 68.49461
> >
> > NSTEP =139795000 *TIME(PS) = 335990.000* TEMP(K) = 299.93 PRESS =
> > -246.6
> > Etot = -116468.7242 EKtot = 28142.6172 EPtot =
> > -144611.3414
> > BOND = 1094.3586 ANGLE = 2907.2089 DIHED =
> > 4540.0461
> > 1-4 NB = 1310.6156 1-4 EEL = 14286.1251 VDWAALS =
> > 16100.2964
> > EELEC = -184849.9921 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 12061.4866 VIRIAL = 14481.3696 VOLUME =
> > 454452.8877
> > Density =
> > 1.0350
> > ------------------------------------------------------------
> > ------------------
> >
> > wrapping first mol.: -27.97826 -39.56723 68.53246
> > wrapping first mol.: -27.97826 -39.56723 68.53246
> >
> > NSTEP =139800000 *TIME(PS) = 335999.999 * TEMP(K) = 297.37 PRESS
> > = 2.1
> > Etot = -116224.6694 EKtot = 27902.1836 EPtot =
> > -144126.8530
> > BOND = 1077.4677 ANGLE = 2884.7374 DIHED =
> > 4519.3357
> > 1-4 NB = 1305.2631 1-4 EEL = 14371.2153 VDWAALS =
> > 15909.1364
> > EELEC = -184194.0086 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11897.3296 VIRIAL = 11876.4293 VOLUME =
> > 455201.7252
> > Density =
> > 1.0333
> > ------------------------------------------------------------
> > ------------------
> >
> > wrapping first mol.: -27.98357 -39.57475 68.54548
> >
> >
> >
> >
> > As you can see the output was saved at every 10ps. And after 335990.000
> > ps, the expected next line should be:
> >
> > TIME(PS) = 330000.000 PS. But, it was written as TIME(PS) =
> 335999.999..
> >
> > This point onward, the output is always in ***.999 format, which is new
> to
> > me. I checked the trajectories and the system looks fine.
> >
> > Is it the normal behaviour or there is something wrong ?
> >
>
> This is normal. It is basic round-off error. The primary time unit is
> picoseconds, but your time-step is on the order of femtoseconds -- 0.001 or
> 0.002 ps. However, both 0.001 and 0.002 are repeating decimals in binary
> (which is how computers store numbers), which means that those two numbers
> are *impossible* to represent exactly by a simple floating point variable.
> So to the computer, the time step is *very close* to 0.001 or 0.002
> (whichever you chose), but not exactly the same. If you add that
> difference up 330,000,000 times (or 165,000,000 times for a 2 fs time
> step), you get something close to 0.001.
>
> At that point, the difference appears in the representation of the number
> in the output file.
>
> HTH,
> Jason
>
> P.S., you can demonstrate this with your own program. Here is a C program
> that illustrates exactly what's happening:
>
> #include <stdio.h>
>
> int main() {
> const double dt = 0.002;
> double t = 0;
> long long int i;
>
> for (i = 0; i < 165000000; i++) {
> t += dt;
> }
> printf("t = %.4f\n", t);
>
> return 0;
> }
>
> When I compile this program ("gcc test.c") and run the resulting a.out file
> ("./a.out"), I see the following output:
>
> $ gcc test.c
> $ ./a.out
> t = 329999.9996
>
> --
> Jason M. Swails
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Received on Tue Oct 04 2016 - 06:30:03 PDT
