Jordan Wolfson

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Questions related from Jordan Wolfson

How can I accomplish solvation in GROMACS without using the solvate or genbox tools?

The title pretty much says it all. I am working off of the Bevan Lab GROMACS Tutorial written by Dr. Justin Lemkul. I am not new to gromacs but I am trying to refresh myself on running the...

04 April 2016 1,372 4 View

How to generate new residue information for an .rtp file in GROMACS?

Hello, I am trying to add a new residue so I can run a protein folding simulation using GROMACS. However, I have looked at the aminoacids.rtp file for the force field I want to use and I am not...

06 June 2015 10,142 4 View

How can I join ligands to a protein using gromacs?

I am trying to join glucose and fucose to Thrombospondin 1 (pdb code 1LSL) in order to perform a proper folding simulation. I ran a simulation using the Bevan Lab tutorial from Virginia Tech but...

05 May 2015 5,849 1 View