Carlos G. Oliver

4 Questions 5 Answers 0 Followers

Questions related from Carlos G. Oliver

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...

23 July 2016 2,191 4 View

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 1,611 3 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...

10 February 2016 9,251 1 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...

13 April 2015 1,438 7 View