Why is my Modeled Polymer Breaking during Molecular Dynamics?

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Are these two preparations of phosphate buffer the same?

I am attempting to replicate a HPLC method for the determination of water-soluble vitamins and the mobile phase consists of 0.1M Phosphate buffer (pH 7). The paper states that they made up the...

19 October 2022 1,836 2 View

What methods can be used to measure the phase transition temperature of natural lecithins?

I would like to measure the phase transition temperature of sunflower lecithin from the gel phase to the liquid-crystal phase. The supplier of the product has advised that it is expected to be...

07 April 2022 7,036 3 View

Does selectively reversing variable codes (to achieve uniform sign of coefficients) improve multiple regression in any way?

I was once advised to reverse the coding of any independent variables that have a negative (say) correlation with the dependent variable, so as to achieve the same sign for the coefficients of all...

23 August 2021 3,592 7 View

Unbiased ligand and Enzyme gromacs simulation; what is optimal interaction for covalent inhibition?

Greetings, I have created a number of 100ns ligand and enzyme simulations in which the simulation begins with my ligand within the binding pocket, then over the course of anywhere from 5-20ns the...

29 January 2021 3,830 2 View

How do you edit a m2p file to get nice Dssp images?

I am using the m2p file from https://ringo.ams.stonybrook.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) but my ss.jpg is looking pretty sad I am converting via imagemagick convert ss.eps...

17 January 2021 744 3 View

How to script VMD tcl within bash script?

Greetings, I want to run a vmd script within my bash script. I am using the text only version of VMD for linux for my windows terminal ubuntu subsystem and I would like to generate code within my...

16 January 2021 550 5 View

Can I dissolve freeze-dried catalase and lysozyme in de-ionised water or do I need a buffer?

Can I dissolve freeze-dried catalase or lysozyme directly into de-ionised water or do I need to use a buffer (separate solutions, not both proteins in one)? I will not be storing the solutions and...

10 November 2020 3,400 5 View

How do I report an average standard deviation over multiple samples?

I have a triplicate data set in which each set of data has a mean and standard deviation. I want to report the mean of the means but the error should reflect the standard deviations within the...

26 June 2020 2,708 0 View

Can I remove water from 1-pentanol using RotaVap?

Hi, I am using pentanol as the solvent phase in a liquid-liquid system to create microparticles by dehydration of aqueous droplets. I would like to find a way to reuse the pentanol, which means...

18 February 2020 4,663 0 View

How to minimise protein microparticle aggregation?

Hi, I am creating BSA microparticles in organic solvents using a process known as microglassification. These microparticles are practically pure protein with no additives, stabilisers, surfactants...

08 December 2019 7,263 0 View

Adhesion strength of coating?

How can I determine a good adhesion strength range for coatings on polymer surfaces, such as DLC on polymer substrates? Is there a specific threshold for adhesion strength (from T-peel tests)...

10 August 2024 942 3 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 heat polymer for about 130° without oil bath ?

is there any other way to heat a polymer evenly other than oil bath if so what are those and how to use it

06 August 2024 947 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

How to explain the different interaction between soluble and insoluble polymer in water?

Hello everyone, I am try to understand the differences interaction between insoluble and soluble polymers in water with metal ions and how theit charge density (of metal ions) affect the interaction.

29 July 2024 6,350 3 View

Rituparna Hazra

Hi, one reason could be the inappropriate definition of the bond connectivity and corresponding force constants. Therefore, cross-checking the bond connectivity could be a first step to solve this.

Lourival Rodrigues de Sousa Neto

You need check your force fields files. files .top .itp ..... Jordhan Booth