How to simulate Stockmayer fluid in GROMACS?

I have been studying the dynamics of Stockmayer fluid under various environment. I used LAMMPS for a project. However, I am wandering if there is a way to perform the simulations in Gromacs. Some...

06 July 2019 8,897 0 View

Why LJ-93 potential form for enclosing wall is different in LAMMPS?

I am trying to create a spherical cavity with soft-sphere potential in LAMMPS. However it seems that this cannot be done. There are other options like lj9-3, lj12-6, harmonic etc. The lj9-3 form...

05 June 2018 1,875 0 View

Is it possible to get very high/low average pressure from NVT simulation of biopolymers?

Hello everyone, I am simulating a protein-water system in NVT ensemble using GROMACS. Prior to that I have energy minimised the system using steepest descent and conjugate gradient methods. After...

31 December 2016 623 5 View

Equilibrium Vs. non-Equilibrium MD simulation?

What are the differences between EMD and NEMD? How one decides that which one should be used for a run? I went through some materials available on web but didn't develop a clear concept about...

09 October 2016 2,647 5 View

Is it possible to simulate protein tagged with a dummy point charge (spherical) or point dipole in water ?

07 August 2016 7,704 1 View

How to calculate dynamic structure factor in GROMACS?

Is there any way to get dynamic structure factor from GROMACS ? The static structure factor S(k) can be calculated by taking a Fourier Transform of radial distribution function g(r), but I...

07 August 2016 3,867 5 View

Is there any way to extract electrical dipole moments of individual solvent molecule in GROMACS ?

I need the trajectory of individual dipole moment of ~104 water molecules to calculate single particle dipole-dipole auto correlation function. "g_dipoles" can give dipoles of the total system or...

06 July 2016 8,568 6 View

Is there any way to read MD trajectories from a .xtc file (generated using GROMACS) in a FORTRAN code?

I am trying to read trajectories to calculate some properties from a .gro file generated after "trjconv" on a .xtc file in GROMACS. This will be required in a FORTRAN90 code. But the .gro file...

06 July 2016 1,464 12 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

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Irradiation data for JAPAN?

Hi, Could you help me to get the latest (2019, 2020) solar resource data for a particular site in JAPAN? PV GIS and NSRDB data are not in reach to JAPAN, I'm looking for some other database for...

03 March 2021 961 3 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 to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 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

Why do the air flow results vary totally when adding scalar in CFD ?

Dear All, We are using Autodesk cfd to calculate the air flow in a single sided naturally ventilated room, where air flow depends only on buoyancy due to temperature difference between inside and...

25 February 2021 9,602 4 View

How to model Supercritical water gasification (SCWG) process in Homer software?

Hi everyone How to model Supercritical water gasification (SCWG) process in Homer software?

25 February 2021 4,075 1 View

Steps to calculate activation energy by coats & redfern method?

I'm a chemistry student and I'm researching the kinetic degradation of mixed plastic waste. I'm having trouble calculating the activation energy by the coats & Redfern method. The data that...

24 February 2021 974 1 View