On Tue, May 7, 2013 at 5:47 AM, Deák Robert <kokumetto.gmail.com> wrote:
> 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?
>
I highly doubt there is a bug here. All irest=1,ntx=5 does is load the
velocity array from the values taken from the restart file. Furthermore,
it's arguably one of the most frequently used bits of code in Amber, since
most simulations begin as a restart from the previous (except for initial
simulations and heating following minimization dynamics).
It's far more likely that the edits you are making (which are non-standard
and possibly error-prone) have some subtle issue with them that's causing
this effect.
Good luck,
Jason
--
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
Received on Tue May 07 2013 - 06:00:05 PDT
