How to generate infinite system in gromacs usibng pbc ?

Lata Rani @Lata_Rani

03 March 2018 0 5K Report

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

Badges
Science topic

More Lata Rani's questions See All

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

Analyse peptide-water interaction from gromacs trajectory

Kindly suggest how to analyse H-bond between peptide and surrounding water molecules from a gromacs trajectory file.

04 May 2017 845 2 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

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

Hello Everyone ! I'm looking for a good journal to publish my manuscript with low publication cost?

I am Looking for a Science Journal with good impact factor and low publication cost to publish a review paper. Your suggestions would be appreciated.

06 August 2024 6,796 3 View

Is Galaxy.org good to use for research for analyzing data and for publication?

Hello all, I wanted to know, can I use galaxy (USA, Europe or Australia) platform for analyzing the shotgun data, and can it be used for publication purpose as well? Thanks :)

06 August 2024 6,610 4 View

How to convert a privately loaded document into a public document?

I attempted to make a privately uploaded text public but a window appeared that said an error occurred. There was no explanation provided as to why there was an error or what might be done to...

05 August 2024 8,025 7 View

How to analyze multiple phosphorilation sites?

Hello, I am currently analyzing some phosphoproteomics data, but I have peptides with multiple phosphorylation sites or phosphorylations together with carbamidomethylation or oxidation. How can I...

04 August 2024 8,432 3 View

How to send my account link and how to make my account public?

Nothing

01 August 2024 755 1 View

Recovery rate after peptide desalting using Sep-pack C18 1 cc Vac Cartridge?

Recently I'm trying to use Sep-pack C18 1 cc Vac Cartridge (Waters: SKU: WAT054955) to desalt digested peptides. However, the recovery rate is usually 40-60%. What is the normal recovery rate?

31 July 2024 6,544 11 View

How can productivity (using the Google form link below to provide your answers) be achieved in manuscript publication?

Survey on Productivity in Journal Manuscript Publication Survey Form Link: (https://forms.gle/YRVrn8dL4WZJJ79S8 ) Dear Researcher, We kindly invite you to participate in our survey focused on...

29 July 2024 4,116 1 View