Can anyone tell me how i can reterive complete bacterial data from KEGG?

I Want to download complete KEGG bacterial data please guide me how i can do that? or if any one have this data kindly send me. its not freely available for academic user too.

06 July 2019 8,918 6 View

Does PME requires periodic boundry condition using extend or restart file in namd?

Hi, I have a protein complex system, Initially i have minimized and equilibrate my system for 0.5ns. Then i want to slowly relax the side chain and back bone of my protein. i used all the restart...

09 October 2016 7,416 3 View

What is meant by Umbrella sampling and why it is require for PMF calculation in MD Simulation?

Hello, I want to know about umbrella sampling, and why it is required for potential of mean force for MD simulation?

08 September 2016 3,121 2 View

Which tools can plot inter-hydrogen bond interactions graph?

i want to plot total number of inter-molecular H_bond interactions between the drug compounds and target protein like below mentioned...

07 August 2015 4,118 13 View

Why Gromacs 4.5.6 does not generate .xtc file?

06 July 2015 6,637 9 View

How to convert amber topology and cordinates files into gromacs topology and cordiante file?

Hello, I want to run protein ligand MD simulation using Amber99sb force field. i generated protein topology files using gromacs easily but when i generated ligand topology using AmberTools15 and...

05 June 2015 4,816 3 View

How do I calculate binding free energy of simulated antigen-antibody structure?

I want to calculate binding free energy of antigen-antibody complex after 30ns MD simulation. I used MMPBSA but it takes approx 12 days for 1 ns (500 frames) of antigen-antibody complex in which i...

01 February 2015 3,036 15 View

Which is the best computational software to remodel antigen-antibody?

I downloaded PDB ID 4I3S it contains 16 missing residues in heavy chain of antibody as well as in antigen. I want to remodelled it before running the simulation. Which is the best computational...

10 November 2014 5,217 10 View

How can I calculate the half life of an inter-hydrogen bond?

06 July 2014 1,104 0 View

How can I calculate inter-hydrogen bonding between an antibody and antigen using pymol?

i want to calculate inter-hydrogen bonding between antigen and antibody using pymol. how i can calculate it and how i can get the hydrogen bonding log file?is there any way to get pymol log file...

05 June 2014 6,962 3 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View