Can someone recommend a MD force field for phosphorylated cysteine (3-oxoalanine)?

I would like to do classical MDS of a protein containing phosphorylated cysteine (3-oxoalanine) using GROMACS. Which force field should I use?

07 August 2019 7,344 4 View

Why Gromacs mmpbsa shows 'nan' in energy values?

I have performed simulation using gromacs. The protein is of two chains, I am trying to understand the changes in mmpbsa values between the two chains but I get following. What could be possible...

02 March 2019 1,935 3 View

Is it possible to create gromacs ndx file of two chains as a single index file?

I have performed a protein-protein simulation. I wish to see the change in binding between protein chain A & chain B. How to create a index files of chain A & B and do the analysis? Like GROUP 1 :...

02 March 2019 6,250 4 View

Can GROMACS perform molecular dynamics with different pH? If NO, what could be an easiest alternative?

I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I...

01 February 2019 3,095 5 View

Is it possible to draw the nano particles using software? If yes, what are they?

We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...

02 March 2018 7,111 1 View

Could someone suggest a tool to find druglikeness of multiple compounds at a time (.sdf)?

05 June 2017 8,517 0 View

Why many of the drugs in market do not satisfy lipinski rule?

05 June 2017 2,142 5 View

What are the set of parameters and its normal value used in "Quantitative Estimate of Drug-likeness (QED)" predictions?

05 June 2017 7,745 0 View

When considering molecular dynamics simulation, which is more appropriate? A long run dynamics or multiple run dynamics?

03 April 2017 2,597 3 View

How to find the average distance moved by metal from the protein using Gromacs?

02 March 2017 541 2 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

What is Nano technology with coronavirus helpe the human..and is it nano mterals removal of covid19?

I anwar by adsorption or reaction ..but it is either more method...

02 March 2021 4,811 2 View

How to compare different concentrations of nanoparticles for characterization from ICP-MS?

I took measurements of different concentrations of 15 nm and 5 nm Au nano particle solutions. I'm trying to determine which concentration I measured gives the best reading overall. I also...

02 March 2021 7,626 1 View

Discrete Phase model (DPM) particle break-up has particle size limits during particle tracking?

Hello, I am currently working on simulating water droplet partciles in a closed room. When I use uniform particles, without "particle break-up", I can carry out the simulation without any problem....

02 March 2021 3,053 2 View

Distribution of particles in metal matrix?

How would define the "good" and "poor" distribution of particles within the matrix. Is there a quantitative solution to assess the distribution of the particles, which then having denotation of...

28 February 2021 7,397 8 View

Is there a deep reason for using the squared modulus of the wave function as the probability density of the existence of the particle?

I think we were all surprised at the first time we got to know quantum mechanics that the squared modulus of the wave function is the probability density of the existence of the particle? The role...

28 February 2021 6,282 9 View

LEDs on Vis Light photo degradation of MB water sol via N doped TiO2 in a mini flume?

Good day to all, I have no experience with light emitting diodes. I am building a glass mini flume to demonstrate the photo degradation of Methylene Blue in water running over self cleaning...

26 February 2021 4,026 5 View

Zno nano particles colour changed from white to grey in process of calcination any suggestions?

In the formation of Zno nano particles process, after drying at 120 degree C, my zno nano particles are completely white but when i calcine it for 450 degree C it converts into grey colour. i...

26 February 2021 2,435 4 View

Why there are two peaks while using the mie plot of Silver nanoparticle?

Hi, I am trying to learn the theoretical modelling of silver nanoparticle using the Mie scattering theory. After that, I discovered a software named Mieplot developed by Philip Laven, where it...

25 February 2021 7,493 6 View

What software programs can directly simulate Additive Manufacturing Directed Energy Deposition (DED)?

I understand there are a lot of software programs that can simulate DED by going through specific modeling, simulation, and commands. For me, that was time consuming and results were not accurate....

24 February 2021 4,428 3 View