Marawan Ahmed

5 Questions 15 Answers 0 Followers

Questions related from Marawan Ahmed

Autodock Particle Swarm optimization algorithms?

Did any one work with the Particle Swarm optimization algorithms built over Autodock, such as PSO@Autodock, FipsDock and Sodock. I would like to know the virtual screening performance in real...

09 September 2015 6,850 5 View

Is anyone familiar with minimizing the RMSD between two proteins in MD simulation?

I have a protein homology model which I am currently running MD simulations for. I am asking if there is a way to force this protein to adopt a certain conformation of another homologous protein...

10 October 2014 5,124 7 View

PMF between two different hosts

I want to do an MD simulation to see the transition of a ligand molecule between two hosts. My first host is a cyclodextrin (Drug carrier), the second host is Albumin. I would like to see if the...

09 September 2013 8,605 5 View

NAMD or GROMACS for membrane protein simulation?

Which is better for membrane protein simulation: NAMD or GROMACS? If someone has a experience regarding the ease of set-up, availability of the analysis tools, accuracy, etc please let me know

08 August 2013 5,610 2 View

Is it reasonable to simulate two/three systems simultaneously in the same MD run?

I want to push a bound ligand from a host carrier to a protein active site using SMD and PMF and i want to trace the free energy change associated with this process. Can I think about it as a...

08 August 2013 7,104 2 View