Rmsd analysis in Gromacs?

More Urszula Sylwia Uciechowska-Kaczmarzyk's questions See All

Equlibration errors in GROMACS input file?

I am trying to run equilibration i gromacs 5.0.7 Implicit solvent. My input file is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps =...

11 December 2017 6,620 0 View

Does anyone know a software/application that can be used for preparing a pictures of sequence alignment?

I am looking for a software for preparing nice (publication) pictures of sequence alignment.

02 March 2016 9,185 8 View

Any advice on single strand DNA in hairpin conformation?

Does anyone know how to build a ssDNA in hairpin conformation? Does anyone know maybe other software where I could do this? Thank you in advance for any suggestions.

01 February 2015 8,333 6 View

How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

22 January 2015 5,376 2 View

Why do I get this error while running psfgen for NAMD?

I want to run dsDNA-protein MD simulations. I have tried to use top_all36_na.rtf Iprepared a script to run psfgen: package require psfgenresetpsf topology charmm36.nbfix/top_all36_na.rtftopology...

31 December 2014 171 9 View

How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

31 December 2014 1,169 2 View

How can I determine the Hbond occupancy with GROMACS?

Dear Gromacs users, I would like to run H-bond analysis in order to get a percentage H-bond occupancy between protein and DNA. How can I do it? I used the g_bond command but the obtained plot does...

29 October 2014 5,219 13 View

With regards to Gromacs Radius of gyration, how do I analyse the data?

Does anyone know how to analyse the plot obtained from gyration? I know what it means but I'm not sure how to use this measure or interpret data? I run MD for a protein in complex with DNA.

21 October 2014 9,021 1 View

Is it possible to run RMSD calculations in GROMACS?

Is it possible to run RMSD calculations for the part of the protein for example rmsd for AA 45-187? How to specify it using g_rms command?

15 October 2014 901 5 View

CAS with GROMACS, tutorial availabe?

Does anyone know if there is a tutorial for Computational Alanine Scanning using GROMACS?

09 October 2014 5,735 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 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 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

Problem in energy minimization using Gromacs?

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

RDF calculation of water inside the Carbon nanotubes?

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

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

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