How to perform PCA Principle component analysis, MMPBSA after MD simulation using Desmond ?

12 February 2023 0 2K Report

I have performed 300ns md simulation using Desomond, is there any script or tools available in desmond for perfroming the PCA and MMPBSA anaysis. I have tried conversion using Intermol tool but no proper output was obtained.

Badges
Science topic

Similar topics
Filing

More Varun T K's questions See All

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,840 0 View

How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

07 August 2024 5,307 1 View

Do we save MSMEs of the Nation ?

SMEs are backbone of the country's white economy, most of them are II generation entrepreneurs and migrated from family owned business policies, and having sufficient higher educations for...

01 August 2024 5,562 2 View

How to perform EEG source analysis on each trial of data separately?

Hello Everyone I have a question about structure for connectivity analysis on sources. My goal: preprocess and cut data into trials create headmodels, using template MRI file perform source...

30 July 2024 2,743 1 View

Is VSM measurment of NdFeB alloy powder sample require any spesific sample preparation ?

Is any specific sample preparation required to perform VSM measurement of NdFeB alloy powder to get a square-shaped M-H loop? Or is it mandatory to make magnetically aligned and sintered pellets...

09 July 2024 1,967 0 View

How to see whether my protein is aggregated using western blotting?

I am working on one protein which gets aggregated (similar to alpha-synuclein and tau) in certain neurodegenerative diseases. I am trying to confirm the aggregation using Western blotting....

30 June 2024 5,060 3 View

How can i calculate the band alignmet of Sc2CO2/BlueP heterostructure from DFT?

I know the work function and band gap of each monolayer and heterostructure. I calculated mulliken electronegativity(X) of Sc2CO2 and Bluep. From that i found Ev = X- 4.5+Eg Ec = Ev-Eg, where Eg...

28 June 2024 9,360 0 View

Please let me know where I can study the scaling effects of experimental studies on soil slopes in geotechnical engineering?

I am looking to simulate real-world landslides in a laboratory setting and measure parameters such as volumetric water content, pore water pressure development, seepage patterns, and ground...

23 June 2024 8,340 2 View

How to get Consistency Ratio when scale of relative importance is used in AHP?

In AHP (Analytical Hierarchical Process) using 9 criteria, when I use a a scale of relative importance (1-9), I am getting a higher lambda-max and hence an inconsistent Consistency Ratio (>.10)...

16 June 2024 1,225 1 View

Can we use any inferential statistics on a data set measured using non-validated questionnaires?

I have heard from my senior scholars that we can't use a non-validated scale to measure variables in a correlational study. Is it true? Can anyone help me with finding a reference for the same.

05 June 2024 7,848 4 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,493 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,726 4 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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,703 7 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 3,142 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 780 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 1,089 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 3,083 8 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 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 672 3 View