How can I create a topology in Gromacs for a small alcohol molecule?

Greetings I'm trying to use the drude forcefield in gromacs for a small alcohol molecule.I tried to follow the topology of aminoacid as an example. I put drude particules in every Carbon atom and...

10 November 2018 4,009 0 View

How to obtain surface charge density from experimental data?

Greetings, I need the surface charge density of particulate solid at diferent pH. I have tried from the surface complexation model but there are several things missing. I only have the zeta...

08 September 2018 318 3 View

What basis is proper for aluminum oxide?

31 December 2016 8,600 4 View

Is it possible to use an OPLS potential in conjunction with other potentials originally created with an arithmetic mixing rule for sigma?

I'm using Gromacs 5.0.2 for a MD simulation with polymer in a saline solution, but the parameters for the polymers are not know, so I'm using OPLS, but this create a incompatibility with the other...

03 April 2016 9,257 4 View

How to rendering HQ images in VMD with polyhedra drawing method?

Hi I try to create an HQ image with VMD with the Tachyon option, but when I try to render an error message appear when the molecules are drawing with polyhedra...

01 January 1970 1,523 1 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

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Hello every body Does any one has any idea to help me choose a reasonable basis set for intermediate metal ions (i.e Fe2+, Mn2+, Cu2+ and exc.) interactions with guanine or other DNA organic...

01 March 2021 6,187 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

Which polarizers are usually used to measure the birefringence of zebrafish muscles?

I already found several publications on that topic, however, the specifications for the used filters are often missing. Some more specific information than "fish is placed between to polarizing...

23 February 2021 1,934 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 formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View