Lata Rani

6 Questions 9 Answers 0 Followers

Questions related from Lata Rani

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

04 April 2018 5,261 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

03 March 2018 4,495 0 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.

05 May 2017 820 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.

02 February 2017 5,669 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...

01 January 2017 279 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...

05 May 2016 1,014 2 View