Steven,
Can you email me directly your inputs ? mdins, prmtop and crds so I can
take a look.
Thanks !
Steven Winfield wrote:
> 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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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project and Department of Chemistry
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Wed Jan 23 2008 - 06:07:17 PST
