What is the default ion concentration in gromacs?

02 March 2016 5,898 7 View

Why is the -pq of calcium showing +1in gromacs while adding 2mM calcium ion concentration in the system?

hello all, i have a system with 122046 water molecules and i want to add 2mM calcium ion concentration to the system. The current net charge on my system is -3. Now, i am trying to use the genion...

31 December 2015 9,583 1 View

Which forcefield suits the best for divalent metal ions like calcium in protein system?

which forcefield suits the best for divalent metal ions like calcium in protein in gromacs system and why. the calcium makes bidentate bonds with protein and water.

09 October 2015 233 1 View

Is minimization required after MD simulations also?

05 June 2015 3,814 6 View

Can anyone help me with analysis of my NPT simulation in gromacs?

03 April 2015 4,852 4 View

How can I generate distance restraints between metal ions and its coordinating protein chain residues in gromacs?

can anyone please help me in guiding how to generate distance restraints between metal ions and its coordinating protein chain residues in gromacs. If i make index groups of my metal ions and use...

03 April 2015 9,739 8 View

Can Na+ ions used to neutralize the system diffuse into the protein in gromacs simulation?

02 March 2015 6,354 6 View

How can I solve the problem in restraining bound water in protein in gromacs?

i want to perform simulations in gromacs using gromos53a6 forcefield. when i apply positional restraints to ions. it gets invoked. but now i want to restrain bound water for which i have generated...

01 February 2015 7,288 5 View

Is anyone familiar with the use of the Force constant in mdp file?

I'm interested in doing a bunch of runs with slightly different restraint forces, I have certain queries regarding this: 1) how can I set a force constant and change it according to my need by...

01 February 2015 2,675 1 View

Can anyone help me with Refcoord scaling in gromacs?

hello all, I used refcoord scaling=com in npt equilibration and now running production phase with positional restraints on calcium ions in my protein when i get this warning: "you are using...

31 December 2014 9,884 2 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