[gmx-users] multiple time step
gmx3 at hotmail.com
Wed Jun 30 09:45:44 CEST 2010
Our philosophy up till now is that with bond constraints and hydrogens
replaced by virtual sites one can reach a time step of 4 or 5
femtoseconds. This is roughly equal to the largest time step, used for
the PME mesh part, in multiple time stepping. But we then do less
work on the non-bonded and bonded interactions. Therefore we think
that out aproach is somewhat more efficient.
But we are thinking about implementing multiple time stepping as well.
I already implemented proper reversible multiple time stepping for
the typical Gromos twin-range non-bonded force setup for the 4.5
> Date: Wed, 30 Jun 2010 01:41:01 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] multiple time step
> I recall seeing something online about how gromacs developers have
> decided to focus on increasing the overall speed and allowing
> generally large timesteps (via e.g. angle constraints) vs.
> implementing multiple timestepping (no mailing list ref. sorry). I
> agree that this is not a logically exclusive decision -- PME takes
> >20% of the time so if they were doing it only 1/2 as often then
> there is the possibility of a real speedup. Nevertheless, it would
> need to be tested and perhaps the developers have indeed run these
> tests -- I've simply not seen the results. One would think, though,
> that PME could nearly always be done less often than, for example,
> bonded interactions.
> I agree with Erik that the work would be large, but I disagree that
> the benefits would be small -- although I suspect that neither of us
> has any data to support such claims :).
> Unfortunately, the bottom line is that this is free software and if
> you want it then you can code it. Or at the very least, you should
> benchmark the benefits on NAMD and then submit an "enhancement"
> -- original message --
> The core developers have the answer for this one, but I can make an
> educated guess:
> Implementing it would mean a LOT of work and the rewards are small. The
> latter because most particles will have rougly the same oscillation
> period if one uses all-atom forcefields and turn on virtual sites and
> constrains the bonds, hence the point of having multiple time steps is lost.
> Vitaly Chaban skrev:
> > Chris,
> > An interesting question...
> > BTW, is there any philosophy of gromacs developers to avoid this
> > algorithm in the MD engine?
> > Vitaly
> >> multiple timesteps are not possible as far as gromacs 4.0.7. NAMD
> >> can do this.
> >> -- original message --
> >> Is it possible to carry out multiple time step molecular
> >> dynamics simulations
> >> in Gromacs
> >> 4.0. versions ? Could you
> >> please give me some information about this issue ?
> >> Thank you very much for your attention.
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