Messages

31

General Questions and Answers / QM/MM simulations

« on: November 23, 2020, 12:30 »

Hello,

I know that QuantumATK has the possibility for doing both MM and QM simulations. I want to know if there is the possibility of doing QM/MM simulations in ATK. In this simulation method you can choose a part of system for QM simulations while the calculations for other parts of the system will be MM. This method is very useful when size of  the system under study is large, yet you are interested in chemical reactions and bonding in a specific part of the system.
Thank you in advance.

Best regards,
Hadi

32

General Questions and Answers / ERROR when I try to open ATK

« on: November 20, 2020, 14:59 »

Hello,
I have been using Quantum ATK on Win10 with no problem. The software crashed suddenly and now when I try to open it again I receive this ERROR:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "zipdir\NL\GUI\Main\Main.py", line 291, in main
  File "zipdir\NL\GUI\MainWindow\Project\OpenProjectWidget.py", line 590, in launchProjectBrowserOnStartUp
  File "zipdir\NL\GUI\MainWindow\Project\ProjectHandler.py", line 72, in currentProject
  File "zipdir\NL\GUI\MainWindow\Project\ProjectHandler.py", line 113, in projectList
  File "zipdir\NL\GUI\MainWindow\Project\ProjectHandler.py", line 113, in <listcomp>
  File "zipdir\NL\GUI\MainWindow\Project\Project.py", line 67, in __init__
  File "zipdir\NL\GUI\MainWindow\Project\Project.py", line 86, in setPath
  File "build\lib\ntpath.py", line 544, in abspath
ValueError: _getfullpathname: embedded null character in path


Would you please help me???
Thanks
 

33

General Questions and Answers / Re: QuantumATK2019 won't open on Linux(mint) on VirtualBox

« on: November 18, 2020, 09:14 »

Nobody to help me with this please???

34

General Questions and Answers / Re: QuantumATK2019 won't open on Linux(mint) on VirtualBox

« on: November 13, 2020, 13:21 »

Thank you very much for your response. The problem with linux has been solved but the other problem is remained.
Both ATK on my windows and on the cluster are 2019 release. I attached the .py file and the error please find the attachment.
Thank you again.

35

General Questions and Answers / Re: QuantumATK2019 won't open on Linux(mint) on VirtualBox

« on: November 12, 2020, 10:46 »

Another problem and another way to solve my problem:

Actually I have been a windows ATK user. I have it on windows and I prefer to use it on windows. The problem is this:
I create a script with the ATK on windows and save it as a .py file. Then I want to run this .py file on the ATK on our department cluster and it gives some errors like it doesn't recognize some commands in the .py file. However, the cluster doesn't have any problem with the input files (.py) made by linux version of ATK! So I assumed I have to switch to linux version of ATK on my system. Actually, If I can solve the problem of running .py files made by windows version of ATK on the ATK on the cluster, I wont need to install the linux version. Why the ATK on the cluster cannot run the .py file made by my ATK on windows properly?!
Sorry for the long story!
THANKS

36

General Questions and Answers / Re: QuantumATK2019 won't open on Linux(mint) on VirtualBox

« on: November 12, 2020, 10:31 »

Thank you very much for your response. I downloaded the bin file and installed it.  I click on the ATK icon on my desktop and nothing happens. It even doesn't ask for license information. No pop-up after finishing the installation. Please find the attachment.
I am looking to your response.
Thanks again

37

General Questions and Answers / Re: QuantumATK2019 won't open on Linux(mint) on VirtualBox

« on: November 12, 2020, 09:22 »

Is anyone able to help me with this please? My work has stopped because of this problem

38

General Questions and Answers / QuantumATK2019 won't open on Linux(mint) on VirtualBox

« on: November 11, 2020, 13:44 »

Hello,
I installed Linux(mint) on VirtualBox on my Laptop. Then I installed the QuantumATK2019 on Linux(mint), but after installation I can not open it and when I try to open it nothing happens. Would you please help me with this problem?
Thank you very much in advance.
Best regards,
Hadi
P.S. I am a quite new Linux user so I will be so thankful if you consider this and give me instructions in details. Thanks again

39

General Questions and Answers / Re: IR absorption spectra

« on: October 5, 2020, 09:41 »

Hi again,
Is there anybody to help me with this question please?
Thanks

40

General Questions and Answers / IR absorption spectra

« on: October 2, 2020, 13:54 »

Hello,

Is it possible to somehow  get (directly or indirectly) the IR absorption spectra of a sample in QuantumATK? I am trying to obtain the IR absorption spectra of  a ZnO treated surface.

Looking forward to your responses.
Thank you
Hadi

41

General Questions and Answers / Re: Considering the effects of a solvent in interactions

« on: September 4, 2020, 10:47 »

Thank you very much Brad, for your great responses.

42

General Questions and Answers / Re: Considering the effects of a solvent in interactions

« on: September 1, 2020, 09:40 »

Thank you very much for your complete and helpful response.

Unfortunately ReaxFF is the only predefined potential that is available in ATK for my system. I was thinking of defining a potential set for my system manually but I suppose it will be so difficult to do that accurately for getting reliable results.

I will be so grateful if you help me set DREIDING step by step.

In terms of DFTB calculations, I think as you mentioned correctly it is too computationally costly.

Best regards,
Hadi

43

General Questions and Answers / Re: Considering the effects of a solvent in interactions

« on: August 28, 2020, 14:17 »

Hi Brad,
Thank you very much for your very helpful and comprehensive response. Please find the attachment. Thanks.
Hadi

44

General Questions and Answers / Considering the effects of a solvent in interactions

« on: August 26, 2020, 14:30 »

Hello,
I am using Quantum-ATK to investigate the adsorption of a protein molecule (Albumin) on a surface of a slab like ZnO or diamond. Because of the large size of the system, I am using forcefield simulations. I did some simulations with the assumption of the protein molecule being in vaccum and over the surface of the slab. Now, I need to consider the protein being in a solvent (not vacuum)  and over the surface of the slab. I intend to go for implicit solvent strategy (although it is not accurate). These are my questions:

1. how I can introduce a solvent to be around my protein molecule instead of the vacuum?

2. Is using the different dielectric constant for the space (currently vacuum) above the surface a good idea for doing that? If yes how can I do that?

3. I used forcefield simulations so far (for the molecule in vacuum). What kind of calculations should I use for the molecule in solvent? Is using forcefield still possible? Generally would you please guide me on choosing the proper calculator in Script Generator for the new case? I need the
calculations be as fast as forcefield if it is possible.

Thank you very much for your responses in advance.

45

General Questions and Answers / Re: I need to have albumin molecule on ATK

« on: August 17, 2020, 14:55 »

Thank you very much. It has been solved by your guide.