I am a beginner in the field of GROMACS.
I want to study the adsorption mechanism of citrate, oxalate, and pyrocatechol on hematite nanoparticles in the pH range of 9-5. Moreover, I want to study the presence of different electrolytes...
09 October 2018 7,260 3 View
I have created ZnO cluster in GaussView by increasing the lattice parameters in all three dimensions with total number of atoms as 32. Is it possible to know the size of this cluster from the...
02 March 2016 8,634 1 View
I am trying to simulate dppc lipid bilayer using OPLSAA forcefield. I downloaded 128-dppc.pdb, 128-dppc.top, dppc-opls.itp and opls-ua-lipid atomtypes.itp (contains only atom types) files from...
03 April 2015 5,915 5 View
Is free version of CRYSTALMAKER software available for download? I downloaded demo version but that does not allow to save file.
03 April 2015 4,861 2 View
I converted the pdb file to mol2file using openbabel 2.3.2. When I am trying to execute the topology of the file using the following command: ./topolbuild -dir...
03 April 2015 5,464 12 View
I created iron pyrite nanocluster in material studio 7.0 and exported it as .pdb file. I downloaded martinize.py to convert this nanocluster to coarse grain and create simultaneously cg.gro and...
02 March 2015 1,485 4 View
I want to build coarse grain model for metal oxide nanoparticles using GROMACS. CNT simulation steps are available on gromacs site (Andrea Minoia's tutorial) but I need steps for metal oxide...
02 March 2015 5,740 3 View
GROMACS
05 June 2014 2,024 1 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
