How to create a coarse grained model of a protein and ethanol using martini forcefield ?

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How to use polarizable force fileds like Drude in NAMD ?

As stated in NAMD tutorial it is presently beyond the capability of the Psfgen tool to generate the PSF file needed to perform a simulation using the Drude model. So how can we generate suitable...

05 June 2019 6,638 1 View

In NAMD, should the flexible cell option turned on during NPT simulation ?

I am confused about setting the cell basis in NAMD. Initially, I set the cell basis according to my solvation box dimensions + 2 or 3A to separate the unit cells in the PBC. This is fine during ...

04 May 2019 8,915 5 View

How can I calculate the torsion angles of a specific residue side chain over MD trajectory in VMD?

I performed a 100 ns MD of a protein in an organic solvent and I want to calculate the change in torsion angles of a specific residue side chain over the simulation. is there any script to do that ?

06 July 2018 1,709 1 View

Namd OR Gromacs?

I have been using NAMD for one year now and I haven't used GROMACS yet. For those who used both of them, which one is more efficient?

04 May 2018 9,380 2 View

How can an organic solvent improve an enzyme activity ?

It has been known that most of the organic solvents have a detrimental effects on enzymes activity and structure but, if incubation of an enzyme in a specific organic solvent lead to an increase...

02 March 2018 5,838 6 View

What is the best concentration to study the effect of an organic solvent on enzyme?

I am studying the effect of different organic solvents on lipase stability. To compare the wild-type enzyme with it's mutants in terms of stability, should I work at very drastic conditions like...

02 March 2018 2,456 5 View

How can I run a repetition of MD simulation using NAMD ?

I performed a 50 ns production simulation for a protein in an organic solvents using NAMD. Now I want tp run a repetition for the simulation. I read about different approaches but I confused. can...

01 February 2018 2,049 7 View

SEM analysis of an immobilized enzyme on Eupergit C 250 L

I am going to carry out SEM analysis for my immobilized enzyme ( Alcohol dehydrogenase) on Eupergit C 250 L (epoxy-polymer). Any recommendation or precautions during sample preparation process?

05 June 2017 3,515 1 View

Using Bradford assay at very low protein concentration ?

Actually I am immobilizing my Enzyme ( an alcohol dehydrogenase ) on Eupergit C 250 L . In order to determine the amount of enzyme that didn't bind to my matrix , I use Bradford assay to...

03 April 2016 3,887 6 View

How do large proteins fold?

i mean is there any difference between the folding mechanism of large proteins and small ones ?

10 November 2014 1,363 4 View

What are the long-term impacts of incarceration on youths' developing brain?

I want to explore the long-term effects of incarceration on a youth's developing brain. I also want to explore research that looks critically at incarceration and punitive measures as the primary...

12 August 2024 862 0 View

How to calculate CCS for Sodiated adduct ions and Multiply Charged Ions?

I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...

08 August 2024 8,329 0 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

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

What is the solvent for 8YSZ nano material?

I need to do some experiment with it in liquid form.

07 August 2024 613 3 View

How does grain and grain boundary affect the ceramic when studying its dielectric properties?

I am not able to get good literature and the physics behind how first these grains and grain boundaries arises out of no where when we make a pellet to study its dielectric properties and then how...

07 August 2024 5,177 3 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 Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

What should Berlin do as a city to become as impactful as London and Paris in World Football?

Please go through my Abstract. I can also share a proposed Thesis Outline.

04 August 2024 2,077 0 View