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Re^9: Are there any Specific basis sets for ions?

Solntsev Pasha

Dear Siddheshwar.

I would suggest you first to run simple job, say water optimization. Open output file and read it line by line. You will better understand what FF is doing at each stage.

Good luck.


On Sat Dec 8 '12 6:32am, Siddheshwar Chopra wrote
>Thank you so much for making things clear to me. Whe nyou open the Benzene.out file with "MasK"...Go to "Extended Summary" option..There in the window you will find "optimization completed: NO". I will not rely on these softwares now. I would be grateful if you could send me some most important keywords to be searched every now and then..
>On Fri Dec 7 '12 6:26pm, Solntsev Pasha wrote
>>Dear Siddheshwar.

>>Graphical programs useful for some particular tasks, but not for all. You should look first into your output file with any text editor. Make sure job was terminated without errors, equilibrium geometry is located and so on.

>>Unfortunately, there is no official GUI program for Firefly and some compatibility issues may rise with available programs.

>>On Fri Dec 7 '12 2:42pm, Siddheshwar Chopra wrote
>>>Dear Fabian,
>>>First of all let me thank you for a detailed explanation. As I am new to FIREFLY, I used MASK for reading the output of the file I have just supplied to you. In MASK, there was "NO" written in front of the option "Optimization Completed". In addition when I used the same output file for the "Single Point Energy" Calculations, I got the final file, but with a message that Stationary point is not reached..Hence this output is invalid... This confirmed my doubt... Sir please check the output file (Benzene.out) with "Mask" and let me know if i m correct or not.
>>>Also please find the PDF file of the paper in which I read about the Benzene-Li+ interaction and help me understand it.
>>>On Fri Dec 7 '12 11:57am, Fabian wrote
>>>>Dear Siddeshwar,

>>>>I don't see your problem with your output, it says: ***** EQUILIBRIUM GEOMETRY LOCATED *****. I also can't find the text "Optimization not completed".

>>>>For fixing charge on one atom: I wonder what would be the sense in that? I guess you want to calculate the interaction of Li+ with benzene. The predominant interaction of benzene with Li+ is probably the pi-sytem of the benzene ring donating electron density to the Li+ and thereby reducing the carge on the lithium somewhat. By fixing a charge of exactly +1 to the lithium this wouldn't be possible.
>>>>Perhaps you can tell us where you read about Benzene-Li+ which isn't [benzene-Li]+ ?

>>>>On Fri Dec 7 '12 6:38am, Siddheshwar Chopra wrote
>>>>>Thank you sir. The symmetry used by you is C6, whereas I have used C1. Regarding my another doubt of SPECIFIC ATOM CHARGE..I have read in a paper where it was mentioned--- Benzene-Li+ and not [Benzene-Li]+. Sir could you have a look at the Benzene.inp and Benzene.out I have supplied here, which is not optimizing at all. I dont know why. The same Benzene is optimizing well in Gaussian03, with Lan2LDZ basis and minimum energy comes around -232 Hartrees. But here it says "Optimization not completed". Please help.

>>>>>On Thu Dec 6 '12 6:50pm, Solntsev Pasha wrote
>>>>>>Dear Siddheshwar.

>>>>>>Please find in the attachment simple input file for [Li(C6H6)2]+. Symmetry restricted to be C6. Please, adjust all parameters according to you task. If you need to use basis set, which is not available in Firefly, you can download it from (GAMESS-US).

>>>>>>BTW, as far as i know, you can't fix charge on particular atom. You specify charge for overall system for geometry optimization.

>>>>>>On Thu Dec 6 '12 4:48pm, Siddheshwar Chopra wrote
>>>>>>>Thank you Sanya for the information. Actually i dont know how to add charge to specific atoms in a complicated molecule..say for example lithium ion in between a benzene molecule.. i have the cartesian coordinates for benzene..could u please send me an input file with a lithium ion between a benzene??
>>>>>>>One more question Sanya... can i use basis set "LAN2LDZ" fin firefly...because i dont see it included in any software, mask, avogadro etc??? I optimized a benzene using gaussian03...but i am unable to optimize it in firefly...i dont know why...i did many changes but not successful.please help...
>>>>>>>On Thu Dec 6 '12 3:09pm, sanya wrote
>>>>>>>>All standard basis sets (including built-in ones) contain basis functions for lithium. It makes no matter whether it is ion or neutral atom, the basis set is the same. Just set proper nonzero ICHARG for ionic species and be careful to match charge and multiplicity.

>>>>>>>>On Thu Dec 6 '12 1:10pm, Siddheshwar Chopra wrote
>>>>>>>>>Dear Sir, I know this question is not directly related to Firefly, but as I am using Lithium ions for study, I was curious to know if there are specific basis sets in MASK or AVOGADRO which must be used to study Lithium ion containing molecules? Also could you tell me how to change the CHARGES of specific atoms only?

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