How can I make a decision among AutoGrid, AutoDock, LAMMPS and AMBER for MD simulation of DNA?

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Why does my DID stain some organelles besides the cellular membrane?

I stained MCF-7 breast cancer cells with DID following the manufactorer's protocol (20 nM for 20min). However, it is found out that some organelles were stained besides the cellular membrane. I'm...

09 October 2019 564 5 View

How to deal with mycoplasma in cell cultures?

How to deal with mycoplasma contaminant in cell cultures? The growth of my cells was obviously hampered.

07 August 2019 7,420 3 View

Dose EDTA influence the cell internalization of nanoparticles?

I am focusing on the cellular uptake of some nanoparticles. These particles can only stably exist in buffered systems containing EDTA. It has been reported that EDTA influence the permeability of...

06 July 2019 3,883 1 View

How to sterilize liquids (containing thermal unstable components) with really small volume?

I am testing antibacterial properties of a peptide of which the mass is as low as tens of microgram. If I want to set a wide range of concentration, I have to dissolve the peptide powder in a...

04 May 2019 774 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 1,495 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

How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 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