[gmx-users] protein wandering away AND binding free energy

Nancy Deng jdeng at adrik.bchs.uh.edu
Thu Mar 24 18:35:34 CET 2005

Thank you very much,  David,  for your quick response and comment, and thanks Dallas for your suggestion to use "VMD" and "trjconv" to center the protein back into the water box. I would like to try that very soon.

I have one more question that from output (.edr, .trr) of a ligand-protein complex MD study, may i calculate the binding free energy of small ligand???? If possible, what's the command, please???


  ----- Original Message ----- 
  From: Dallas Warren 
  To: Discussion list for GROMACS users 
  Sent: Wednesday, March 23, 2005 2:16 PM
  Subject: Re: [gmx-users] protein wandering away

    I just simulated a 5ns MD by GROMACS FF for a small system containing 160
    amino acid residues in a water box. The thing confused me was that the
    protein started to close one edge of the water box around 2ns and part of it
    movedout of the box later. At the end of the 5ns calculation, most of
    protein was out of the box, while water molecules were still in the box.

  That is just the PBC acting.  The water molecules are so small that, pretty much as soon as they wander out of the box visually, they then reappear on the opposite side.  However, with something as large as a protein, as it moves out the side of the box, to visually keep it within the rest of the water, you would have to break the molecule.  And that isn't done, so it seems that the protein is sticking out into a "vacuum".  But if you check the opposite side of the box, there will be a hole in the water where the protein molecule is inserted.  Using VMD you can easily turn on the boxes in each periodic direction, so that you can easily see that happening.

  Just used trjconv to center the protein back in the simulation box if you want to.

  Catch ya,

  Dr. Dallas Warren
  Department of Pharmaceutical Biology and Pharmacology
  Victorian College of Pharmacy, Monash University
  381 Royal Parade, Parkville VIC 3010
  dallas.warren at vcp.monash.edu.au
  +61 3 9903 9574
  When the only tool you own is a hammer, every problem begins to resemble a nail. 


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