Carlos G. Oliver

8 Questions 7 Answers 0 Followers

Questions related from Carlos G. Oliver

How is subspace overlap interpreted in a Molecular Dynamics simulation?

I am looking for ways to estimate whether my simulation has sampled for long enough and I came across the subspace overlap calculation (Hess, 2002) which compares the covariance matrices of two...

07 July 2016 9,887 4 View

Can two ends of a protein artificially touch each other by crossing box boundaries?

I am running simulations of a short peptide in GROMACS 4.6 and I noticed that my peptide stretches out to almost cover the whole diameter of the dodecahedral box. I am wondering if the periodic...

07 July 2016 6,222 7 View

How do I get the protein in the center of the box in gromacs?

Hello, I am solvating a short peptide with a dodecahedral box using the following GROMACS 4.6 commands: pdb2gmx_mpi -ignh -f $1.pdb -o $1.gro -p $1.top -water spce -ff oplsaa editconf_mpi -f...

07 July 2016 2,546 5 View

What replica exchange MD temperature range and transition probability is appropriate for a large (470 amino acid) simulation?

I would like to simulate a large globular protein of 470 amino acids using replica exchange. I have seen in literature that for larger proteins it is better to use lower transition probabilities...

02 February 2016 1,616 1 View

How do I generate distance matrices for specific frames in trajectory with GROMACS g_mdmat?

I would like to generate individual and mean distances for a trajectory using g_mdmat from GROMACS. That is, I have a list of time points in the simulation (which are not interspersed at a regular...

09 September 2015 5,595 1 View

What are the combs on DNA gel electrophoresis stations made of?

I am just wondering what material(s) is/are used for the combs in DNA electrophoresis gels since they are so expensive. To be clear, the comb is the small seemingly plastic piece that has 'teeth'...

07 July 2015 4,954 2 View

How do I extract a PDB structure from a GROMACS simulation by Radius of Gyration?

I would like to extract a structure from a GROMACS simulation at the timepoint corresponding to when the peptide is at its highest radius of gyration. Is there a way to do this without having to...

05 May 2015 8,172 3 View

How do I modify the temperature in Molecular Dynamics simulations with GROMACS?

I am trying to run a 34 amino acid peptide through very high temperatures to denature it. Other publications have done this at 600 K so I am trying to do the same. To do so I simply edit the...

04 April 2015 2,325 8 View