If I wish to stop an MD simulation (AMBER) in between, what command I need to use to write/extract .rst file ?

More Pavan K Madasu's questions See All

How to use Desmond in HPC ?

Our department has recently acquired an HPC (High-Performance Computing) system, and I'm thrilled to take my molecular dynamics calculations to the next level using Desmond. I used to run my...

28 July 2024 6,553 1 View

What should I consider as the equivalent weight and density when I testing corrosion rate of aluminium electroplated with nickel?

Hello everyone, I am actually performing a corrosion rate analysis for a sample of aluminium that is electroplated with nickel. I am using Linear Polarisation using the Palmsens EmStat 4s...

26 February 2024 3,319 2 View

What is the difference between a Chemical Vapour Deposition (CVD) system and Chemical Vapor Transport (CVT-Zone furnace) system?

06 February 2024 9,845 3 View

The metal complex I synthesized has a crystallinity index % of 99%, so is my doubt valid?

The metal complex I synthesized has a crystallinity index % of 99%, this data if obtained from Origin. software by using powder XRD data so is my doubt valid? If yes what does mean that? Thank you

31 January 2024 5,284 0 View

Which analytical method is good for determining the composition of an impure potassium formate salt?

Hello, I actually have a salt of potassium formate, but the issue is that there are many impurities in the salt. I wanted to know which analytical technique is appropriate to quantify the...

23 January 2024 5,055 14 View

What would the effect of Potassium Formate be on corrosion?

Hello, I was testing the corrosion rate of Aluminium when dissolved in a highly concentrated potassium formate. Now I know corrosion rate is influenced by the presence of dissolved oxygen as well...

18 January 2024 5,424 2 View

Why does phosphorylation decrease while total protein level increase?

Therapeutic intervention (agonist) increases total protein level, however, phosphorylation is decreased (neutralized by total protein). What would be the possible reason? If anyone has any paper...

16 January 2024 9,963 1 View

Whether it's possible to create a TIC (Total Ion Chromatogram) using only specific phytocompounds from High-Resolution Mass Spectrometry (HRMD) data?

04 December 2023 4,126 1 View

How to slove : "Search path GAUSS_EXEDIR is "C:\G16W" in DFT ?

Hi this is G. Pavan I'm trying to do a DFT calculation of small molecules, but I'm not succeeding in getting optimization data, It showing me that "Search path GAUSS_EXEDIR is "C:\G16W" . How can...

25 August 2023 4,944 1 View

What is the concentration of antibiotic for PCR 2.1 TOPO cloning?

Ampicillin 50ug/ml is what specified in the kit, means should I use 5 grams of ampicillin for one liter of LB agar?

15 August 2023 7,603 2 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 1,494 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

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 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 1,092 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