[CP2K:9646] The charge set for QM/MM MD simulation

Junbo Lu luju... at gmail.com
Sat Nov 11 16:38:41 CET 2017


Thank you, Teodoro. I have looked at this section. How can I define the
function to make sure Cl- in MM section.
Best regards,
Junbo

2017-11-08 17:05 GMT+08:00 Teodoro Laino <teodor... at gmail.com>:

> please have a look at the section : https://manual.cp2k.org/
> cp2k-3_0-branch/CP2K_INPUT/FORCE_EVAL/EXTERNAL_POTENTIAL.html
>
> On 8 Nov 2017, at 08:51, Junbo Lu <luju... at gmail.com> wrote:
>
> 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
>> 显示删减掉的内容
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to cp2k+uns... at googlegroups.com.
>> To post to this group, send email to cp... at googlegroups.com.
>> Visit this group at https://groups.google.com/group/cp2k.
>> For more options, visit https://groups.google.com/d/optout.
>>
>>
>>
>> --
>> You received this message because you are subscribed to a topic in the
>> Google Groups "cp2k" group.
>> To unsubscribe from this topic, visit https://groups.google.com/d/to
>> pic/cp2k/0YL4lM9Rqj8/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> cp2k+uns... at googlegroups.com.
>> To post to this group, send email to cp... at googlegroups.com.
>> Visit this group at https://groups.google.com/group/cp2k.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at https://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "cp2k" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/
> topic/cp2k/0YL4lM9Rqj8/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at https://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20171111/67fefc44/attachment.html>


More information about the CP2K-user mailing list