How to build the topology files for Broken DNA?

hello, I want to do gromacs simulation of a protein DNA complex along with a small molecule ligand. But unfortunately the bound ligand is not a complete one..its one helix is cut. So, i am...

11 December 2018 3,742 6 View

Why one chain break are connected during the energy minimization?

We have placed a dimer protein into gromacs energy minimization utilising OPLS force fields. but after running 9567 its get minimized. But the problem is that after energy minimization one gap...

11 December 2018 8,799 4 View

Fatal error: Syntax error - File ligand.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes?

I want to perform a protein-DNA-ligand complex simulation by gromacs. but my system contain two ligands named PTR and LIG. but when ever i am going to perform the energy minimization. This is...

11 December 2018 4,118 2 View

Protein Homology modelling?

I have a trimeric protein which have a lots of missing residues. that why i decided to build homology modelling. but after successfully modelling each chain contains maximum loop like structure...

03 April 2018 8,272 5 View

What is the reason for increasing RMSD?

I have a protein containg 2138 amino acids in each chains. then i added POPC membrane and then add solvent ater and counter kcl ions..then i had done 025ns run for eqilibration by restrating...

08 September 2017 3,045 5 View

Protein-Ligand-DNA simulation

Hello Everyone, I have a AUTODOCK docking PDB file for both Protein-Ligand-DNA Complex. I want to do simulation of these complex. but simulation failed due to unrecognized ATOM TYPES present into...

05 June 2017 5,315 5 View

Protein-ligand simulation in Gromacs

05 June 2017 7,607 15 View

Steered Molecular Dynamics?

11 December 2016 4,458 1 View

Why TLR7 specific antagonist is not found right now?

we didn't find any specific TLR7 specific antagonist . maximum are dual antagonist of TLR7 and TLR9 antagonist. Is there any specificity on the protein active site? what was the reason for that?

08 September 2016 8,478 6 View

Does anybody help to pull multiple atom of trimeric protein in SMD in NAMD?

I am doing SMD of protein using NAMD with constant velocity pulling. In order to do the simulation, we have to specify the smd-atom (the atom to which the dummy atom is attached and then pulled)....

07 August 2016 6,599 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

Does the circuit modeling for planar monopole antennas using Foster canonical forms give good approximation?

Hi researchers, I am searching for some accurate way to do the circuit modeling of planar CPW-fed monopole antennas. I have gone through the literature where mostly circuit modeling is done using...

28 February 2021 7,016 1 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