Can anyone advice how to troubleshoot segmentation fault (core dumped) during NVT equilibration stage of ligand- protein simulation?

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How do I generate topology of many ligands which are not coonected all of them ,for gromacs?

Hi. I want to do simulate via gromacs for ligand- protein complex which there is 9 ligands (three of them are seperated and six of them are connected together(picture in Add files). when I used...

31 December 2019 7,687 5 View

How I can neutralize my system with counter ions, in combination with a physiological salt concentration?

I am a new Gromacs user . I want to do simulation of laccase with its ligand (N-acetyl-D-golocosamin)(NAG) which is a suger whith gromose 54a7 and I use the ATB server for production of ligand...

11 December 2019 8,452 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

No amplification data for qPCR on MxPro?

I have set up a qPCR run on MxPro with SYBR green and ROX as a reference, however, when I go to the analysis section the program seems to only collect data for the dissociation curves and not the...

25 February 2021 8,039 1 View

IF troubleshooting: looking at an intracellular protein that localizes to the cell's and how to reduce increase in signal due to cell ruffles?

I am currently trying to stain for PI3KBeta in MDA-MB-231 cells. My current issue is that 1) beta stains all over the cell and 2) there is an increase in signal at the edge of the cell and this...

24 February 2021 8,582 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

In methylene blue test Why is UV absorbance reading very low as soon adsorbent is added and then increasing before reaching equilibrium?

Hello, I'm working on removal of methylene blue. 01. in the dark test very first reading is taken 15 minutes after adding adsorbent to the dye solution and that UV absorbance reading is very...

19 February 2021 472 5 View

Justin Lemkul

The maximum force is unreasonably high. Check the coordinates around the atom on which mdrun reports this force for bad contacts or perhaps an indication of an inadequate topology.

Jamoliddin Razzokov

Have you performed an energy minimization run? Check one more time concordance of topology and coordinate file.