CP2K tutorial for biochemical systems

[Dries Van Rompaey]

Hi cp2k-users,

After experimenting with cp2k for a while I have written down a short tutorial on how to use cp2k for biochemical systems. The tutorial covers the setup of an enzyme system with ambertools followed by equilibration with cp2k at the MM level, after which we move the system to QM/MM for metadynamics simulations of an enzymatic reaction. I am far from an expert myself, but I thought this might be useful to people starting out. If you spot any mistakes or something that could be improved, please let me know. The tutorial can be found at https://driesvr.github.io/Tutorials/ as well as on the main cp2k wiki: https://www.cp2k.org/howto:biochem_qmmm. 

Kind regards

Dries

[Ole Schütt]

Hi Dries,

your tutorials are indeed very nice and they fill an important gap our
documentation concerning QM/MM. Usually, we collect tutorials centrally
on our wiki: https://www.cp2k.org/howto . Could I interest you in moving
them there? The conversion from Markdown to DokuWiki should be straight
forward.

In any case, thanks a lot for the work you already put in!

Cheers,
Ole

On 2017-07-18 08:49, Dries Van Rompaey wrote:
> Hi cp2k-users,
>
> After experimenting with cp2k for a while I have written down a short
> tutorial on how to use cp2k for biochemical systems. The tutorial
> covers the setup of an enzyme system with ambertools followed by
> equilibration with cp2k at the MM level, after which we move the
> system to QM/MM for metadynamics simulations of an enzymatic reaction.
> I am far from an expert myself, but I thought this might be useful to
> people starting out. If you spot any mistakes or something that could
> be improved, please let me know. The tutorial can be found at

> https://driesvr.github.io/Tutorials/.
>
> Kind regards
>
> Dries
>
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[Dries Van Rompaey]

Hi Ole,

Sure, I'll put them on the wiki as well. Thanks for the comments!

Dries

Op dinsdag 18 juli 2017 13:14:20 UTC+2 schreef Ole Schütt:

[jts2t...@gmail.com]

Hi Dries,

I have read the tutorial and wonder how could I show the advantage of QMMM calculation over MM calculation. Should I run a complete MM simulation and compare the two results ? I notice that you said in the tutorial that the reaction is not achieved in the simulation. Does that mean QMMM method doesn't work in this simulation ? 

在 2017年7月18日星期二 UTC+8下午2:49:11，Dries Van Rompaey写道：

Hi cp2k-users,

After experimenting with cp2k for a while I have written down a short tutorial on how to use cp2k for biochemical systems. The tutorial covers the setup of an enzyme system with ambertools followed by equilibration with cp2k at the MM level, after which we move the system to QM/MM for metadynamics simulations of an enzymatic reaction. I am far from an expert myself, but I thought this might be useful to people starting out. If you spot any mistakes or something that could be improved, please let me know. The tutorial can be found at https://driesvr.github.io/Tutorials/.

Kind regards

Dries

[Dries Van Rompaey]

Hi,

The MM simulations in the tutorial are intended to allow the system to relax and to find suitable cell dimensions. We do this at the MM level because it's rather fast when compared to QMMM. The relaxed system is then moved to the QMMM level in order to simulate bond breaking. 

The reaction is not sampled in the unbiased QMMM, which is why we add metadynamics in the second part. Once we bias the collective variable, you can see the reaction occurring at the QMMM level.

Op woensdag 19 juli 2017 13:34:52 UTC+2 schreef jts2t...@gmail.com:

[jts2t...@gmail.com]

Thanks for your reply, Dries !

The first paragraph you said is understood. I also wonder how does one know the reaction really occurs in the simulation ? i.e. Which part of the output file is important to know the information about the reaction ?

I major in  calculation mathematics, therefore the easy thing for you may seems hard for me.

I'll appreciate for your reply !

在 2017年7月19日星期三 UTC+8下午8:00:59，Dries Van Rompaey写道：

在 2017年7月19日星期三 UTC+8下午8:00:59，Dries Van Rompaey写道：

[Dries Van Rompaey]

Hi,

You can observe the reaction occurring by visualising the xyz files of metadynamics qmmm simulation - you will see the C-O bond breaking and the C-C bond forming. You can also plot the collective variable in the metadynlog file: the 3 to 8 bohr region is occupied by the substrate and the -3 to -8 region is occupied by the product.

Hope this helps,

Dries

Op woensdag 19 juli 2017 15:12:14 UTC+2 schreef jts2t...@gmail.com:

[jts2t...@gmail.com]

Thanks for your patience !

在 2017年7月19日星期三 UTC+8下午9:40:39，Dries Van Rompaey写道：

[Dries Van Rompaey]

You're welcome.

The tutorial has been updated with a brief section on how to include enzyme residues in the QM region. As always, comments and improvements are welcome.

Op donderdag 20 juli 2017 03:15:40 UTC+2 schreef jts2t...@gmail.com:

[Qing Feng]

Hi Dries,

    Thanks for you tutorial on biochemical systems. After seeing this tutorial ,I make some try on RNase systems. In order to save time ,I only chose four bases for simulation. But when I simulated a full QM/MM system, 

I got the following error.

  *******************************************************************************

  Translating the system in order to center the QM fragment in the QM box.

 WARNING| Particles:    5387     93 at distance [au]:     0.82969217 less than:      0.95400000; increase EMAX_SPLINE.

 *******************************************************************************

 *   ___                                                                       *

 *  /   \                                                                      *

 * [ABORT]                                                                     *

 *  \___/                GEOMETRY wrong or EMAX_SPLINE too small!              *

 *    |                                                                        *

 *  O/|                                                                        *

 * /| |                                                                        *

 * / \                                               fist_neighbor_lists.F:607 *

 *******************************************************************************

   I don't know why this problem occur .   Could you help me to see if there are any problems.

   

  For helping your understanding, I attach my files. Thank you in advance!

  

  Best wishes!

  

  Qing

 在 2017年7月18日星期二 UTC+8下午2:49:11，Dries Van Rompaey写道：

Hi cp2k-users, 

[Tianshu Jiang]

Hi Qing,

The same situation occurred in my run, but it is remained to be solved.

Have you solved the problem in your simulation afterwards ?

在 2017年12月14日星期四 UTC+8下午9:27:48，Qing Feng写道：

[qingh...@gmail.com]

Hello Dries,

Thanks for your tutorial! Could you please comment on changing ZERO LJ parameters to "0.3019 0.047"?

Have you done some tests on it? What's the effects of the modification on water itself? Thanks a lot!

All the best,

Qinghua

[Sam Broderick]

Hi

I love Dries' comic-like molecules. Does anyone know what he used to do this?

Thanks

Sam

[Bowen]

I get the same problem after changing ZERO LJ parameters to "0.3019 0.047" for water molecules, TYR and SER. 

changeLJSingleType :TYR@HH 0.3019 0.047
changeLJSingleType :SER@HG 0.3019 0.047
changeLJSingleType :WAT@H1 0.3019 0.047
changeLJSingleType :WAT@H2 0.3019 0.047
change charge :41@N  -0.41427
change charge :41@H  0.27333
change charge :41@CA  0.02273
change charge :41@HA  0.11383
change charge :41@C  0.59873
change charge :41@O  -0.56647
change charge :145@N  -0.41427
change charge :145@H  0.27333
change charge :145@CA  -0.05667
change charge :145@HA  0.13743
change charge :145@C  0.59873
change charge :145@O  -0.56647