In the study of swelling clay and factors affecting swelling.
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
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
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
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
Hi all, i am presently working with a system containing NaCl and i added some Calciumchloride to see the influence of change in cation. Now i have my results but i'll like to know how i can study...
08 September 2017 1,933 3 View
07 August 2017 1,757 11 View
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
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
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
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
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
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
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
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
I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.
18 February 2021 4,822 2 View
I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...
17 February 2021 1,066 3 View
I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...
15 February 2021 5,561 3 View
