Hello all,
Thank you all for your advice so far. A few more items:
Jason, are there parts of your dissertation that are already published? My
avoidance of gaining a deeper understanding of Amber 12 is catching up with
my project. I have mainly used the Amber 12 reference manual and outdated
amber tutorials. To everyone, what are some good resources, links etc., for
learning and understanding how to use Amber 12 effectively and
understanding, to a reasonable extent, what is under Amber 12's hood, e.g.
how prmtop files are generated, their format, and how Amber 12 uses them to
run simulations and analysis.
Hopefully this question is not too general for this forum.
Thanks,
David
On Thu, May 16, 2013 at 12:15 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, May 16, 2013 at 11:49 AM, David Winogradoff <dwino218.gmail.com
> >wrote:
>
> > Hey guys,
> >
> > Thanks Jason for the thorough reference. I am currently comparing 2
> prmtop
> > files, and their LENNARD_JONES_ACOEFF (& ...BCOEFF) sections are almost
> > identical with a few discrepancies. In your reference, you comment that
> > there are [NTYPES X (NTYPES + 1)] / 2 entries. Could you explain why
> there
> > are this many entries and how to know which pair of atoms corresponds to
> > which entry?
> >
>
> NTYPES x (NTYPES + 1) / 2 comes from combinatorics. The A and B
> coefficients are pairwise terms, so each term corresponds to an interaction
> between a pair of atoms (think of it as a matrix of dimension NTYPES by
> NTYPES where each matrix element A_i,j is the A-coefficient between atom
> types i and j). This matrix is symmetric (since the X->Y interaction is
> the same as the Y->X interaction). Therefore, you only need half of the
> NTYPES^2 terms. You also need to include the diagonal of that coefficient
> matrix, which is where the extra +1 comes from (so you really need slightly
> more than half of the matrix elements: half of the non-diagonals and all of
> the diagonals).
>
> There's also a note in those sections that tells you to refer to the
> ATOM_TYPE_INDEX and NONBONDED_PARM_INDEX sections to see how the ACOEF and
> BCOEF sections are indexed.
>
> The topology file is a complicated beast. There are a few sections with
> real 'parameters' (bond force constants, equilibrium values, angle
> parameters, dihedral parameters, LJ parameters, charges, and masses). Most
> other sections are filled with pointers into various other sections of the
> topology file. It is a strong reflection of how the energy and force
> routines were originally implemented in Amber, but it does not make for a
> human-friendly file format.
>
> While I will certainly not urge against learning the intricacies of the
> prmtop file, I will warn against trying to grok topology files of large-ish
> systems directly. I would consider myself to be an expert on prmtop files,
> and even for trivial questions, I typically use a program to extract the
> information I want. I find ParmEd quite helpful here (in large part
> because I wrote it) -- there are a variety of commands available to extract
> almost any kind of information you want (including the ability to write out
> an frcmod file with all of the parameters contained inside).
>
> HTH,
> Jason
>
> P.S. One other comment: 'diff' (and meld, vimdiff, etc.) are very limited
> tools for comparing prmtop equivalence. Obviously if 2 files are
> identical, so too is the energy function defined by those prmtops.
> However, 2 prmtops can give identical energies, yet be completely
> different according to diff tools.
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue May 28 2013 - 09:00:04 PDT
