Any successful story for the bio-degradation of Thiocyanate from laboratory to Field ?

Because many scientist groups are working on this problem. Success rate at laboratory level had been reported but at field level hardly we will find any story.

10 November 2017 9,028 0 View

Anyone familiar with MD simulatios using Gromacs ?

I have a .pdb file, in this file when I want to use pdb2gmx command> there is this error massage:> Fatal error:> Incomplete ring in HIS680Ask What should to do?

06 July 2015 5,114 12 View

Can anyone help with MD simulations using Gromacs?

During add ions steps using Gromacs the overall charge on my protein was calculated qtot -35 So i have to add positive ions to neutralize the charge on protein. then i have added 35 Na ions using...

06 July 2015 4,497 3 View

MD simulatios using Gromacs?

During MD simulations i got fatal error during energy minimization step after commend: gmx grompp -f minim.mdp -c 2HQA_modified_solv_ions.gro -p topol.top -o em.tpr Fatal error:number of...

06 July 2015 1,963 2 View

How do I study molecular dynamic simulations of a subunit of housekeeping protein of bacteria at different temperature using GROMACS software?

06 July 2015 5,219 1 View

Does anyone know how to operate GROMACS software for analysis of molecular dyanamic simulations using ubantu operating system ?

06 July 2015 4,134 3 View

Can someone help me to short out the problem regarding smear on gel of PCR product?

07 August 2014 2,198 8 View

Please suggest me any journal name to publish my work on in silico (Bioinfomatics) hypothesis regarding adaptation between impact factor 1 and 2

Computational approach

11 December 2013 9,861 2 View

Xylanase bacterial enzyme

I am just starting work on xylanase. Can you suggest an appropriate site for sample collection of xylanase?

05 June 2012 2,534 6 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