AMBER Archive (2004)

Subject: Re: AMBER: <dV/dL> fluctuations in TI

From: Chunhu Tan (tanc_at_uci.edu)
Date: Fri Nov 19 2004 - 13:07:03 CST

Hi, Nelson,

     This page maybe helpful...
http://structbio.vanderbilt.edu/archives/amber-archive/2004/3799.phtml

   Dr. Pearlman's series papers on Gibbs are very helpful, you can find them
on the Gibbs manual reference. The following paper can give you some feeling
about decoupling:
 J. Chem. Phys. V119, 2003. p5740 " Extremely precise free energy
calculations of amino acid side chain analogs: Comparison of common
molecular mechanics force fields for proteins" M.R. Shirts etc.
    So far as I know, when you perturb some charged residues to dummy,
Sander TI may be better, because in Gibbs of AMBER 7 PME had not been used.

   I am sorry to transfer this mail to the list without your permission, but
I think it's better for us to learn from other's view. :)

Regards,
Chunhu

----- Original Message -----
From: "Nelson Fonseca" <nfonseca_at_dq.ua.pt>
To: "Chunhu Tan" <tanc_at_uci.edu>
Sent: Friday, November 19, 2004 1:04 AM
Subject: Re: AMBER: <dV/dL> fluctuations in TI

   Experience is what you get when you don't get what you
 want.
>
> -- Dan Stanford--
>
>
> hi!
>
>
> in fact, I have very close contact in the lasts points of my simulations.
> These arise from the zero force constants used for the dummy dihedrals
> that promote large rotations around some angle giving close contacts
> between Dummy Atoms and regular atoms that still have some residual
> charges (lambda = 0,98). Is there any way to do the decoupling within
> sander? Trying first to do 2 separate jobs- one perturbing the VdW
> parameters and the other perturbing the charges? And the how to compute
> the free energy from the decoupling? Do you have some references about the
> subject? Yesterday I have compiled Gibbs, do you recommend to use Gibbs to
> perform TI or Sander?
>
> Thanks in advance for your help!
>
>
> Regards
>
> Nelson Fonseca
>

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