Postdoc - FAQS.TIPS

More Sayyed Jalil Mahdizadeh's questions See All

Why extrinsic apoptosis never occurs in a normal cell?

I mean why while all the necessary proteins are existed in a normal cell, the extrinsic apoptosis never occurs? Is it because of the hierarchical processes starting with Fas_FADD binding?...

09 October 2019 6,757 3 View

Protein_Protein Interaction prediction through Machine learning?

Hi all, Actually I'm going to evaluate the protein_protein interactions and find the hot spots using machine learning technique. Any decent references and/or suggestions for me as a beginner?

08 September 2019 490 5 View

Code for graphdiyne and graphenylene coordination generator?

Hi all, Does anybody know a code to generate atomic coordination of graphdiyne and graphenylene?

10 November 2018 8,932 0 View

What is the delivery hydrogen uptake?

The delivery hydrogen uptake was specified to the difference between H2 uptake at charging pressure (say 100 bar) and discharging pressure (say 5 bar) both at the same temperature (e.g. 77 K). But...

09 October 2018 4,476 3 View

CPMD of metals?

Dear all, Is Car-Parrinello MD not suitable for zero-band-gaped materials like metals? If so, then why?

06 July 2018 4,944 7 View

Total energy vs. wavefunction's energy cutoff?

Dear all, During the PW-DFT calculations, how do you determine the occurrence of total energy convergence vs. energy cutoff for wavefunctions? I mean is that ok when the total energy difference is...

08 September 2017 2,017 3 View

Free space boundary condition?

What is the free space (aperiodic) boundary condition and how it differs with non priodic one?

05 June 2017 810 0 View

What do you think?

Take your chance to find out what's going on there in time less than 3 minutes. Good luck * All is about the slopes ^_^

31 December 2016 2,072 2 View

What is the difference?

Assume I need a random number between 0-100. What is the difference if I 1. generate a single random number in the range 0-100. 2. generate a single random number in the range 0-10, and square...

31 December 2016 1,866 15 View

MPI error running LAMMPS?

Dear LAMMPS users I was going to run a MD simulation with about 24000 atoms on 8 threads parallel calculations, but I get the following error after 450 cycles: Process 3 exited without calling...

10 November 2016 2,453 3 View

How to calculate CCS for Sodiated adduct ions and Multiply Charged Ions?

I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...

08 August 2024 8,329 0 View

How to use Density Functional Theory to calculate carrier mobilities of solid system?

Hello, everyone. I have tried to determine carrier motilities of some materials, by Density Functional Theory, using Quantum ESPRESSO. There are a few methods to do it, like a package called...

04 August 2024 8,894 1 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

How to Import Blade geometry from CAD file in ANSYS design modeler?

Hello. I have the geometry of a blade in CAD file (stp) and I want to prepare the blade for meshing with turboGrid. I must import this file into designModeler and then transfer to the...

27 July 2024 356 3 View