Dear all,
I sent the email below last week but haven't had any response yet. I
wondered if anyone was looking into this.
Thanks,
Steven Winfield
On 14 Jan 2008, at 15:22, Steven Winfield wrote:
> Dear all,
>
> I'm having a look at AMBER 9's energy conservation when using its
> internal QM/MM code. I took a simple system of pure water (1222
> molecules in total
> in a periodic box of length 34.419A), with one water molecule
> flagged as the QM region (using the PM3 Hamiltonian), turned off
> SHAKE for this molecule and used a 0.2fs time step. The other
> molecules were TIP3P. The input restart file had been equilibrated
> at 300K using 100ps of NVT dynamics with the Langevin thermostat.
> The QM/MM simulation lasted 1ns in total.
>
> I saved the position and velocity data so that I could examine the
> temperature of the MM and QM regions afterwards. I have attached a
> bzipped tar with my input files, an output text file, and some
> temperature plots. Measuring the temperature of a single molecule is
> obviously very noisy, so I also calculated a weighted average of
> temperature values at each point with weights exponentially decaying
> with a time constant of 50ps.
>
> As can be seen from the plot (pme_temp_50.ps) and the text output
> file, I observed a steady temperature increase from 300K to around
> 500K, and the average temperature of the quantum water becomes quite
> large. I tried the same simulation but using a full Ewald sum
> (ewald_temp_50.ps) and observed similar results.
>
> I ran a pure MM simulation with the same input files for comparison
> (with SHAKE on all molecules), because page 143 of the manual says
> that QM/MM with default parameters should "generally conserve energy
> about as well as one would find for a corresponding pure MM
> simulation". I increased the time step by a factor of 10 to 2.0fs,
> which I thought would be on the very edge of becoming unstable, but
> the temperature plot (water_mm.ps) shows no signs of heating.
>
> So my questions are:
>
> What non-default parameters have I used, if any? I've had others
> look at my input files and the only comment I've had is that my
> density may be slightly low. I've kept my timestep small and my
> cutoffs large (9.0A)
> Is there a problem with AMBER's QM/MM code? I'm using a fully
> patched version.
>
> Any comments would be most helpful.
>
> Regards,
> Steven Winfield.
>
> P.S. The input restart file is called 'zeroed' because I wanted
> initially to see if energy was being successfully transferred from
> the rigid MM molecules to the non-rigid bonds of the QM molecule, so
> I manually zeroed the velocities of the QM molecule before starting.
> This shouldn't affect the results though.<heating.tar.bz2>
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Received on Wed Jan 23 2008 - 06:07:16 PST
