MD simulations through web?

More S. Xavier's questions See All

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

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 4,842 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

I am trying to obtain microstructure for Mg-Zn-Sn alloy?

Any suggestions with respect to etchant composition and holding time?

27 July 2024 6,925 2 View

How to get Scopus Author Index ??

18 July 2024 4,080 3 View

Dear researchers. pl help how to plot jablonski energy level graph and magnetic hysteresis curve in origin?

through origin software

17 July 2024 4,991 0 View

Do software tools exist to assess the economic and technical practicality of introducing new food products, such as yogurt with modified starch?

This question explores the world of food innovation and asks if there are computer programs that can analyze the financial and technical feasibility of introducing new food products. For instance,...

13 July 2024 7,446 0 View

My nanoparticle has a lower fluorescence life time of 2 ns (usual life time between 3-10 ns). what are the inferences I can get from this?

what all details we will get from fluorescence life time data

10 July 2024 505 1 View

Alternative binders other than Nafion solution?

Hi Everyone, I plan to deposit a catalyst (TS-1@Co-PDA, in the core: TS-1 zeolite with a shell of Polydopamine designed with Cobalt) on a rotating ring-disk electrode (RRDE) to evaluate the...

29 June 2024 8,203 3 View

Journal Report Impact Factor 2024?

Has the new journal impact factor for 2024 been released? pls send me updates if anyone has it.

19 June 2024 6,333 1 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 1,495 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 7,727 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

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 anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 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

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

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 673 3 View

Krishnendu Bera

Gromacs:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/

Amber

http://ambermd.org/tutorials/

Namd

http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf

For any more help you can write to me.

S. Xavier

Thank you for your response.