How to modify and create a crystal structure (poscar file) for new compound using existing data?

More St Th Jayawardane's questions See All

When I run the package 'foreign' in R, I receive an error message. How do I solve it?

I'm trying to install packages for my masters thesis. When I try to install the package 'foreign' it works but when I try to run it, I receive the message: Error in .helpForCall(topicExpr,...

08 May 2024 7,693 1 View

How should I adjust my HPLC method for a similar column with different dimensions?

I am trying to run a method from a column that is 250x4.6 mm, 8 um particle size into a column that is 300x7.8 mm, 9 um particle size. The makeup of the column is pretty much the same. They are...

29 April 2024 9,983 1 View

Trouble detecting organic acids with LC-RI detector?

I am trying to detect organic acids on my waters LC, which is equipped with a W410 refractor index detector. I am using a Aminex HPX-87H Column which is supposed to work to separate organic acids....

26 April 2024 3,036 1 View

MaxQuant is throwing a configuring error, can someone help me figure out what it means?

I am running MaxQuant and it starts running and almost immediately stops. I go into the error folder (combined-->proc, then select Configuring 11.error). The screenshot of the error is...

14 February 2024 6,348 1 View

Which statistical test to use?

As a Computer Science student inexperienced in statistics, I'm looking for some advice on selecting the appropriate statistical test for my dataset. My data, derived from brain scans, is...

03 February 2024 1,920 5 View

Does Africa need a pan-African news service?

Africa in need of a pan-African news service...

15 September 2023 6,187 0 View

Why is there such world-wide dispersion of certain ancient religious beliefs and practices, ex: sacred Mountains, a Flood, Washings, etc.?

In Christian tradition, mountains are symbolic icons that reference the early temple. Whether the ancient temple itself, or a genuine mountain, the idea of safety, or being closer to God, or as a...

14 September 2023 1,902 5 View

Is Tai Chen right when he says that "Music is the sound of the human mind penetrating the order of human relations?" ???

Music penetrating the order of human relations...

05 May 2023 6,113 6 View

What are the parameters of approximating the molecular weight (MW) of gel electrophoresis bands and comparing them to MW of DNA being investigated?

Agarose gel electrophoresis was run on samples of cDNA obtained from RT-PCR with specific primers, and scans of gel were analysed in Biorad. I'm having trouble ascertaining whether the molecular...

01 May 2023 3,840 2 View

What's the temperature effects on the VASP calculated results?

Dear all, Could you please explain the temperature effects on the electronic properties ( band gap, effective mass and optical properties) in Vasp PBE calculations? I calculated those properties...

19 March 2023 4,062 2 View

How do I replace a file with a more recent version of a paper that was uploaded to ResearchGate?

The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day...

07 August 2024 9,934 3 View

How to solve g_mmpbsa error?

Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out

07 August 2024 6,066 0 View

How do you delete a duplicate pdf for the same paper on ResearchGate?

The first pdf file I uploaded had an error. So I uploaded an updated, corrected pdf of that paper with a different pdf name. I dpon't want the old copy to be download or read.

07 August 2024 9,508 1 View

AUX gas reading problem on QE with full MS and PRM method in one run?

Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...

06 August 2024 4,953 0 View

How to understand this crystallographic phenomenon of low temperature crystals in zeolite?

During low-temperature testing, new diffraction peaks that appear could be indicative of several phenomena. In one of our tests, we observed notable new peaks around 40° and 45° in a specific...

06 August 2024 726 3 View

JCPDS 65-7246 file please?

Dear Researchers Kindly share JCPDS 65-7246 file Thanks in advance

04 August 2024 5,613 1 View

Dirty and clean?

Hi everyone I need a file with a dirty and clean potato image

04 August 2024 7,199 4 View

How to change the version of the article full-text pdf file?

How to change the displayed full article text to its corrected version? In the file on the page of the journal where I published the article, there was an error in the text, the table is...

30 July 2024 3,229 2 View

Why Powder XRD is performed after cruhsing a crystal if Single Crystal XRD analysis of the same crystal has been performed already ?

What information we can get from PXRD analysis other than from SCXRD analysis of a crystal ?

30 July 2024 6,261 4 View

Difficulty with permittivitt and Magnetic Permeability Calculations?

Difficulty with permittivitt and Magnetic Permeability Calculations Hello everyone, I have all the parameters related to the calculations of the permittivitty and magnetic permeability...

30 July 2024 5,206 1 View

Ricardo Tadeu Maia

Hello, St Th Jayawardane

You can create crystal structures using softwares like Diamond and Vesta, but what do you intend to do with these files? And what do you mean by "existing data"? I'm willing to help you, so feel free to send a reply and ask everything you need

Best regards,

Ricardo Tadeu

Yassine El Khessaimi

There are several steps involved in modifying and creating a crystal structure for a new compound using existing data. These steps include:

Obtain the existing crystal structure data for the compound you wish to modify or create. This data is typically available in the form of a POSCAR file, which is a standard format for representing crystal structures in first-principles simulations.

Use a software tool, such as VESTA or CrystalMaker, to open the POSCAR file and view the existing crystal structure. This will allow you to visualize the arrangement of atoms in the crystal and understand its overall structure.

Modify the existing crystal structure as needed to create the new compound. This may involve changing the positions of atoms, adding or removing atoms, or changing the unit cell size or shape.

Save the modified crystal structure as a new POSCAR file. This file can then be used as input for further simulations or calculations to study the properties of the new compound.

Overall, the process of modifying and creating a crystal structure for a new compound involves using existing data to understand the structure of the compound, and making the necessary changes to create the desired structure. This process requires a combination of knowledge of crystal structures and the use of appropriate software tools.