Hi (again) Amber community,
I’ve been running the previous QM/MM simulation with the few changes suggested before and, unfortunately, after some steps, the temperature keeps becoming incredibly high..
I run it, then, without the quantum treatment. The simulation was successfully achieved but when watching the hole system with Pymol, I found out that one of the tree water molecules slip away from the active site. It would only remain in it when restrained with a force of 20 kcal/mol−Å2. Could this “event” be the source of the extremely high temperature and the vlimit exceeded when treating this molecule and others quantum mechanically?
Thanks in advance,
Ruth
> On 11 Sep 2015, at 17:48, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>>
>>> Hi Amber community,
>>>
>>> I’m running a molecular dynamics simulation of a protein with its ligand
>>> and an Mg +2 ion in implicit solvent although there are tree water
>>> molecules in the active region as they are necessary for the reaction to
>>> proceed.
>>>
>>> I’m modeling quantum mechanically (QMMM) a few residues with the PME
>>> method, as well as the Mg ion, the tree water molecules and the ligand
>>> (which contains phosphates).
>>>
>>> The structure has been successfully quantum minimised prior to the MD/QMMM
>>> run and in the later (which, for now, nstlim=1000 only) the initial
>>> temperature is 0°K and the final one is 100°K (tempi=0.0, temp0=100.0)
>>>
>>> I started with dt=0.002 and no shake options. I got an error message which
>>> said: “vlimit exceeded for step..”
>>> and also: "This is usually a a symptom of some deeper problem with the
>>> energetics of the system”
>>>
>>
>> A timestep of 2 fs is about the upper limit of what you can achieve using
>> SHAKE and *no* QM and still have stable integration. It is much too large
>> with SHAKE and QM.
>>
>
> To add a little to this...
>
> 2fs should be fine for QM as long as SHAKE is on. At the end of the day the dynamics are propogated using the same newtonian integration whether you do MM or QM/MM with sander and so the limits on time steps etc should be identical between a purely MM run and a QM/MM run. The issue here is trying to use 2fs with NO shake.
>
> That said this only applies if shake is used for ALL hydrogens. If for example one runs with shake on the MM region but turns it off for QM - e.g. to get triangulated water correct in the MM region but allow a proton to transfer in the QM region then you need to run the calculation as if shake were off for the whole simulation (i.e. 1fs or less timestep).
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Associate Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Associate Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Mon Sep 14 2015 - 03:00:03 PDT
