How to use reduced unit in gromacs?

Dear researchers, I am using gromacs for molecular dynamics simulation. These days, I am working on lennard jones fluid. In lammps, it is easy to use reduced unit by just set the parameter as 1....

01 February 2019 7,304 2 View

Can I make shell script for gmx rdf?

I want to make shell script for calculating rdf. I want to make a lot of rdf.xvg files for each time step. Here's my approach. #!/bin/bash for i in $(seq 1.1 .01 30.0) do echo -e "OH2\nOH2\n"...

11 December 2018 8,965 0 View

How to generate supercritical CO2 in gromacs?

Is there any procedure that I can adapt? or If there's some paper, please let me know. With my respect

10 November 2018 8,116 0 View

How to calculate tetrahedral order parameter in gromacs?

I have 50 ns simulated bulk water system. For analysis, I want to calculate tetrahedral order parameter q. I am using gromacs, and I know the command "gmx hydorder". However, I don't know how to...

09 October 2018 6,779 3 View

Tetrahedral order parameters and local water configurations?

I have configuration simulated with gromacs, NPT for 50 ns. During analysis, I got problems. 1. tetrahedral order parameter q 2. Double donor and single donor configuration division(reference of...

09 October 2018 8,496 0 View

How could I calculate voronoi volue of water?

I am trying to calculate voronoi volume of a water surronded by nearest oxygen. This is my code. from numpy import * import glob box = 3.73014 list_of_files =...

09 October 2018 523 4 View

Does anyone knows how to install drude implementation files for gromacs?

I installed drude implementation files from charmm website. Here's URL: http://mackerell.umaryland.edu/charmm_drude_ff.shtml. On my linux server Downloads directory, I did the procedure 1. git...

08 September 2018 9,901 2 View

Polarizable water model ?

Does anyone know where could I find polarizable water model force field and coordinate file? I looked it up in martini website, but there's no one-bead polarizable model. Rather, they suggest 3...

06 July 2018 5,054 0 View

Could anyone help me inderstanding Soft matter lattice model?

In the lattice model in soft matter physics, average number of solute and solvent pair is calculated by = zNtotV(1-V) where z is coordination number and V is volume fraction for the solute...

02 March 2018 722 0 View

How can i insert molecules inside in gromacs?

I want to insert molecules inside the wall. Configuration is like below. I want to put some ions inside the wall surrounding polymer. Please help me. YK Lee

01 February 2018 9,661 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 to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

How can the modification of garden soil cause global warming?

Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...

02 March 2021 7,161 3 View

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

Does anyone know to clarify these changes?

01 March 2021 1,290 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 convert .vesta file to a .cif file?

I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...

28 February 2021 4,966 3 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 can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials?

Hi, all! How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials? I have not find the choice for explicit element in Abaqus CAE. I am wondering whether it is possible...

25 February 2021 9,936 2 View