I calculated the initial momentum for x, y and z directions for the whole
system, but there is nothing strange. The sum for x direction is -108.92,
for y is 6.36 and for z is 37.42.
I have verified the masses in prmtop, but I changed the masses of all atoms
with parmed. There is also no problem.
I have tried also ntx=5, the results are the same. Of cours for ntx=5 and 7
when I used the rst from equlibration with unchanged masses, I devided the
velocities with 2.
I verified also minimizing, heating and equlibrating the mass increased
system, but with ntx=5 and 7 the situation is the same, the y coordinated
of center of mass in increasing.
With ntx=1, irest=0 there is no problem. So, I think there is something
wrong with ntx=5 and 7 when the masses are changed.
So this might be a bug?
Regards,
Robert
2013/5/6 Jason Swails <jason.swails.gmail.com>
> Does your Arg residue have any initial momentum in the Y-dimension to start
> with (you'd have to calculate that from the velocities in the restart
> file). What about the whole simulation cell? I can imagine that by
> changing the masses of only a portion of the system, you incidentally
> imparted net momentum in the Y-dimension for the unit cell as a whole.
>
> Perhaps you should try setting ntx=1, irest=0 so that the velocities are
> resampled from a Maxwell-Boltzmann distribution (which should have no net
> momentum, or at least very little of it). Does this fix your systematic
> drift in the Y-dimension?
>
> I'll also point out that thermostatted diffusion is not "real" diffusion in
> that it cannot be compared to experimental measurements (you need to run
> NVE with good energy conservation to achieve that).
>
> HTH,
> Jason
>
>
>
> On Mon, May 6, 2013 at 9:25 AM, Deák Robert <kokumetto.gmail.com> wrote:
>
> > Sorry, the input file is here.
> >
> >
> >
> > 2013/5/6 Deák Robert <kokumetto.gmail.com>
> >
> > > Dear Amber users,
> > >
> > > Recently I have done a test.
> > >
> > > The system is a single ARG solvated in a truncated octahedron water
> box,
> > > with a 9A TIP3P water buffer aroud the ARG.
> > > A have minimized, heated to 340 K and equlibrated the system, like in
> the
> > > Tutotial 1, and the production MD (the input file prod.in is attached)
> > > went well.
> > >
> > > Now comes the test.
> > > I have multiplied all the masses in the system with 4 (using parmed).
> The
> > > new dt and taup are doubled and gamma_ln is the half of the earlier
> one.
> > > Theoretically the extracted data for the diffusion of the ARG and the
> > > increased mass ARG (mass x 4) are the same.
> > >
> > > While for the first system everything seems OK, following the center of
> > > mass of ARG (mass x 4) the y coordinate of the molecule is almost
> > > continously increasing, while the x and z shows diffusion like paths.
> > >
> > > Can somebody explain me why is happening this, or this is a bug?
> > >
> > > Regards,
> > > Robert
> > >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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>
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Received on Tue May 07 2013 - 03:00:03 PDT
