up from version 4.6.7 and above.
Not natively, but I think you can do it with PLUMED.
Hello, I'm trying to understand photon shielding parameters such as mass attenuation coefficients (MAC's) and effective atomic numbers (Zeff's). I would like to ask how to calculate for total...
08 April 2020 7,893 2 View
Hello everyone, I' trying to simulate a system with multiple chains. According to the PDB entry, there is a single disulfide bond connecting two of the chains. Unfortunately, 'pdb2gmx' with '-ss'...
18 June 2019 6,599 2 View
Hi everybody. I'm looking for extracted DNA from Curtobacterium flaccumfaciens pv. poinsettia bacteria for positive control. Does someone has it or can tell me there I can get it? Thanks.
02 April 2017 4,034 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
