Re: AMBER: QM/MM Heating

From: Adrian Roitberg <>
Date: Mon, 21 Jan 2008 11:13:18 -0500

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 ( 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
>> ( 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 ( 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
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Received on Wed Jan 23 2008 - 06:07:17 PST
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