[CP2K:9644] The charge set for QM/MM MD simulation

Junbo Lu luju... at gmail.com
Wed Nov 8 08:51:27 CET 2017


Dear Teodoro,
    Thank you for your good suggestion. In option 3, you mean I can apply a
physical restraint. Then how can I apply this spherical wall? By which
keyword in input file?
    Best regards,
    Junbo

2017-11-08 15:22 GMT+08:00 Teodoro Laino <teodor... at gmail.com>:

> Dear Junbo,
>
> first of all many thanks for having posted your request here: more people
> will be able to benefit of the on-going discussion.
>
> Let me explain my point of view regarding your problem, with the
> understanding that they are very much in-line with Juerg’s comment.
>
> First of all as you already realised, the ADBF QM/MM needs to have a
> constant charge and the charge is not allowed to change during the run.
> There is a *very good reason* for that: if you change the charge of the
> QM region you are changing the zero reference for your calculations during
> MD and this makes the analysis of your simulations less trivial.
>
> Therefore, this is not about an "unimplemented feature” (*ignore the
> recommandation received in a separate list, to implement this
> functionality*), rather a protection to prevent users from running
> non-sense simulations.
>
> Once we agree that we need to use the ADBF system with this “limitation",
> let’s move on to your questions.
>
> (1) QM/MM runs do not have to be necessarily neutral. You can run QM/MM of
> QM charged systems (both fully periodic and non-periodic) being extremely
> careful to how you are decoupling the periodic images (in case of fully
> non-periodic calculations). You may have the corresponding counterion in
> the classical (MM) portion and the interaction would still be computed
> correctly (again be careful to decouple the QM part properly), in case
> QM+MM is neutral. You could also have the QM+MM charged and this would
> still work ok.
>
> *Option 1*: I*f you believe that the Cl- is not important for your
> simulation you can freely decide to remove it from the entire system and
> run instead a simulation that is overall (QM+MM) charged (2+).*
>
> *Option 2*: *If you decide to treat the Cl- classically, be sure that the
> Cl- is always far from your Zn2+ center enough (at least 2 solvation
> shells) to avoid any interaction between the two ions that could not be
> treated classically (electrostatic+non-bonded).* In this case your
> overall system (QM+MM) is neutral, with your QM region being 2+ and the MM
> one 2-. Please, use a decoupling to be sure that the strong electrostatic
> coupling between the QM periodic replicas is dumped.
>
> (2) Using ADBF QM/MM for both option 1 and 2 is trivial as your QM charge
> is not changing (and again, for fundamental reasons it should not!).
> *Option 3*: If you start with Option 2, you may notice instead that Cl-
> may play a fundamental role in your simulations or you may already know
> before starting your simulations that you are interested in mapping the
> interaction between the Cl- and  Zn2+.
> In this case, there is only one thing that you can do.* If you believe
> that the Cl- is an important part of the QM center, then you’ll have to
> include the Cl- into the QM region since the very beginning of your
> simulations.* This will have the major drawback that Cl- may leave the
> Zn2+ center with the drawback of being forced to use very large QM boxes.
> Still, there is nothing lost or wasted in life (and in simulations too):
> you can apply a physical restraint (i.e. spherical wall) to prevent the Cl-
> from flying far and subsequently  reweight the calculated free energy
> (assuming you are interested in free energies) for the additional
> constraint. This will help you in containing the size of  your QM box even
> for extended simulation times (several hundreds of ps).
>
> Personally, I like option 3.. but depending on your understanding of the
> system you may decide (equally good) to go for option 2 or option 1. …
> Possibly even for another option not necessarily considered here….
>
> Hope this helps and good luck!
> Best,
> Teo
>
>
>
> On 4 Nov 2017, at 17:07, luju... at gmail.com wrote:
>
> Hi, I want to do a simulation of hydration of Zn2+ by QM/MM MD of CP2K.
> But there are several problems for my simulation:
> (1). I do not know whether we should neutralize the system by minus ion in
> CP2K, such as Cl-. We can also not neutralize the system, is it right?
> (2). If we add some minus ions into system, how can we define the charge
> of dynamic QM region in adbf QM/MM MD calculation? When a charged molecule
> enter the QM region, such as Cl- ion, the total charge of dynamic QM region
> will change. I have read the CP2K manual, I find it can not change the
> charge of QM region when doing MD. So this is a problem.
> Can you help me for these two problems? I will be very appreciated!
> With my best regards,
> Junbo
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