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

[David]

On Thu, 2005-03-24 at 09:35 -0800, Nancy Deng wrote:
> 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???
>  
You can use the LIE approximation (using g_lie) but you need to read
literature about itm, and probably do extra simulations. ALternative is
to use free energy perturbation. See manual.


> Thanks,
>  
> nancy
>  
>         ----- 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
>         Lecturer
>         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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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