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

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

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Justin Lemkul

The better question is - why did you run the analysis? What did you hope that it would tell you? Can some functional or dynamical relationship be obtained from the output?

Faez Iqbal Khan

g_gyrate -s XXXX.tpr -f XXXX.xtc -o gyrate.xvg

Urszula Sylwia Uciechowska-Kaczmarzyk

thank you Saman