29 Questions 123 Answers 0 Followers
Questions related from Sayyed Jalil Mahdizadeh
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?...
10 October 2019 6,699 3 View
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?
09 September 2019 433 5 View
Hi all, Does anybody know a code to generate atomic coordination of graphdiyne and graphenylene?
11 November 2018 8,877 0 View
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...
10 October 2018 4,423 3 View
Dear all, Is Car-Parrinello MD not suitable for zero-band-gaped materials like metals? If so, then why?
07 July 2018 4,893 7 View
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...
09 September 2017 1,966 3 View
What is the free space (aperiodic) boundary condition and how it differs with non priodic one?
06 June 2017 765 0 View
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...
01 January 2017 1,809 15 View
Take your chance to find out what's going on there in time less than 3 minutes. Good luck * All is about the slopes ^_^
01 January 2017 2,027 2 View
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...
11 November 2016 2,406 3 View
Dear all, What is the difference between Car- Parrinello MD (CPMD) and varriable cell CPMD (vc-cp) in Quantum Espresso? Does it mean that the simulation is performing in NPT enssemble instead of...
09 September 2016 2,632 3 View
Dear all Would anyone give me a brief and useful review on VASP and Quntum esprsso? I need to know about their performance, speed, parallel computing, free license and tools. Which one is more...
07 July 2016 481 9 View
Any advice about molecular dynamics simulation application in sea industries?
01 January 2016 4,109 4 View
Dear all Could all atoms zero partial atomic charge be an option for charge equilibration (QEq) method as implemented in LAMMPS? http://lammps.sandia.gov/doc/fix_qeq_reax.html
11 November 2015 6,756 5 View
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06 June 2015 8,878 2 View
Dear all I'm going to evaluate the mechanical response (stress-strain profile) of some materials using molecular dynamics simulation. I found different strain rates result various Young modulus...
03 March 2015 3,476 4 View
Dear all I was calculated the mechanical response of a 5*5 nm graphene sheet by evaluating stress-strain curve (attached file) using molecular dynamics simulation with optimized Tersoff potential...
03 March 2015 5,273 26 View
Dear colleagues I would like to perform a FFT low pass filtration on my 100000 point data in MATLAB? How can i do that?
12 December 2014 443 10 View
Dear all I would like to solvate a single graphene oxide nanosheet using VMD. As i checked it out it need a psf and a pdb file of the solute. Can everybody help me with this issue?
11 November 2014 7,905 6 View
What are the simulation conditions to perform a MD simulation in nano-scale e. g. graphene nanoribbons or semiconductor nano-particles. I mean what would be the simulation box domain? Should the...
10 October 2014 5,692 3 View
Would anybody help me with suggesting a proper postdoc position in theoretical and computational chemistry (quantum or MD simulation or combined)?
10 October 2014 1,988 3 View
I'm going to perform a classical MD simulation on a graphene oxide nanosheet. Everything is ok when I run the simulation without considering coulomb interactions, but when I consider them, the...
05 May 2014 8,856 7 View
This is ~1700 K for bulk.
05 May 2014 692 7 View
I'm going to perform MD simulation on graphene oxide nanosheet. Everything is ok when I run the simulation without considering coulombic interactions but when I consider them the volume diverges....
05 May 2014 5,181 23 View
Dear all Is anybody here who suggest me a well-known supervisor for sabbatical in theoretical and computational chemistry (MD simulation or QM calculations)?
04 April 2014 8,899 0 View
I'm going to calculate the electrical conductivity of some materials (like graphene) theoretically. Do you have any recommendations about suitable theoretical methods or can you suggest good...
04 April 2014 8,986 5 View
Which potential is the best choice for considering the interaction between copper nanoparticles dispersed in water and which one is the best for interaction between water-copper nanoparticles?
01 January 2014 3,974 5 View
As you know, electronic contribution to thermal conductivity for metals is as significant as (or more significant than) phonon contribution (K=Ke+Kph). My question is: do electrons contribute to...
01 January 2014 867 6 View
Fourier transformation of heat current autocorrelation function gives the power spectrum of heat current, which can tell the distribution of the vibrational frequencies (phonon frequencies) that...
07 July 2013 2,519 14 View
