Analyse peptide-water interaction from gromacs trajectory

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How to setup pbc in only z-direction in gromacs ?

Please help for setting up a dimeric peptide infinite only in z-direction with constant distance between periodic images in GROMACS. Thanks Lata

03 April 2018 5,292 4 View

How to generate infinite system in gromacs usibng pbc ?

I want to generate an infinite peptide fibril as has been mentioned in attached publication. I am using gromacs but dont know which options to be used with -pbc option in .mdp file. please help

02 March 2018 4,547 0 View

How to define parameters for solvent Trifluoroethanol for SCRF run using Gaussian ?

I want to perform calculation in solvent 2,2,2-Trifluoroethanol in gaussian but its not defined in gaussian. Please help me out how should I proceed for the same.

01 February 2017 5,711 5 View

Population analysis (Boltzmann distribution) from MD simulation ?

Dear All, please let me know how to perform population analysis (Boltzmann distribution) from MD simulation (in terms of energy). I have Phi/ Psi dihedral values from MD simulations (Gromacs), I...

31 December 2016 304 4 View

How to generate a SER dipeptide with O-GlcNAc (beta- glucosamine) attachment at side chain with OH group of SER ?

How to generate a SER dipeptide with O-GlcNAc (beta- glucosamine) attachment at side chain with OH group of SER. I have genetared the dipeptide with O-GlcNAc , It shows complete dipeptide when...

04 May 2016 1,036 2 View

• What the possible Persistent Organic Pollutants and Heavy metals present in fluorspar, sediments, and water bodies around its mining area?

Approximate concentrations are require in compared with the WHO permissible limts

11 August 2024 2,723 1 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Do interactions between biosphere, carbon cycle, & water cycle impact global warming & interaction between atmosphere & hydrosphere?

How do interactions between the biosphere, the carbon cycle, and the water cycle impact global warming and interaction between the atmosphere and the hydrosphere?

09 August 2024 3,291 2 View

Is it true that $\det(V(A))$ may be only $\pm 1$, depending on $n$, for the last symmetric tridiagonal matrix $A$?

One can try to generalize the Vandermonde determinant in the following direction: Let $A$ be any symmetric $n$-order square matrix. Consider its powers' diagonal elements $(A^k)_{ii}$ and...

08 August 2024 6,690 1 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

Unusual intensity drop in some sections of chromatograms in DDA?

Hi, we have measured tryptic peptides using both DDA and DIA method on QExactive. In DDA replicates i saw unusual intensity drops occurring at the same sections of chromatograms in DDA replicates...

07 August 2024 3,218 4 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