I forget to mention:
The momentum for just the Arg residue is in x direction 16.146, for y
-12.608 and for z 11.382.
R
2013/5/7 Deák Robert <kokumetto.gmail.com>
> 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
>> > >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue May 07 2013 - 03:00:03 PDT
