How to make a descriptive and predictive model?

Hello, I am in the process of making a predictive nonlinear model for my data with one dependent variable and 3 independent variables. I am currently using SPSS and R but the best model i have at...

04 May 2019 1,753 3 View

How to create itp file in gromacs using clayff force field?

Hello all, i would like to generate an .itp file using clayff force field with gromacs. i tried the gmx x2top -f .gro -o .itp -ff command but got error message In command-line option -o...

11 December 2017 7,247 3 View

How to build a clay model?

Hi all, i am currently working on montmorillonite clay. i am using Gromacs, clayff and vmd. i got a unit cell from an online data base but would like to create up to 6 or 16 unit cell model. also...

11 December 2017 3,554 4 View

How to monitor the progress of a simulation in gromacs?

HI all, i am currently carrying out a gromacs simualtion and the simulation has been going on for over 20days because the system is heavy but i will like to know how to check the current state of...

09 October 2017 1,276 7 View

Extending a completed simulation in gromacs?

07 August 2017 1,757 11 View

Temperature dependent simulations in Gromacs?

Hello everyone, i am currently working on the effects of temperature on a system but with my current mdp setting the results are not looking realistic. Curently 300K and 600K are giving the...

07 August 2017 3,179 4 View

What is the command used in the calculation of hydraulic conductivity using gromacs?

In the study of swelling clay and factors affecting swelling.

02 March 2017 1,439 0 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

How the Ground Plane implantation is performed without damaging (and w/o varying the undoped nature) the top Si (8-10 nm) in FDSOI technology ?

It is a general practice to introduce Ground Plane in FDSOI devices under the BoX. The Ground Planes are introduced by Ion Implantation through Top Si layer and Buried Oxide. I wanted to know that...

24 February 2021 5,974 4 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 dissolve cross-linked Amberlite IRC120 H, hydrogen form resin?

Hello all, I have used Amberlite IRC120 H, hydrogen form acidic cation-exchange resin for the ion-exchange of waterglass [sodium silicate solution -- 40% Sodium silicate (mol ratio > 3.2)...

21 February 2021 5,614 3 View

How to prepare electrolyte of NaClO4 salt for Na-ion battery? Any problem with this salt?

Hello, I am trying to make anode for Na-ion batteries. I have no experience with preparation of the electrolyte for any batteries. NaClO4 salt are available and I am planning to use EC:PC as...

21 February 2021 8,132 1 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