Re: [AMBER] questions for mdgx-virtual site

From: David Cerutti <>
Date: Fri, 29 May 2020 05:42:42 -0400

OK, so good evening! mdgx is not going to be FAST simulator but if you
just need to get a system running a few thousand (or even million) steps of
MD then it'll do fine. I am working right now to enable this virtual site
functionality in pmemd and also tleap, so with luck it'll be possible to
create more interesting molecular models in the standard MD engines soon.

For the &rule namelist, it's... a &namelist, just like &cntrl or &ewald in
the sander and pmemd programs. The parser I wrote for it is not
technically the Fortran standard, but it gets things pretty well and lets
you have some flexibility. I would try writing this first:

  frame1 = "C1",
  frame2 = "C2",
  epname = "VSB",
  style = 1,
  v12 = 0.5,
  sig = 2.1,
  eps = 0.05,
  residue = "UNK",

In your input, you have lots of colon punctuation (:) that mdgx won't know
how to parse (nor will sander or pmemd). And I've written the above in
shorthand. There are aliases for all those keywords if you find one or the
other easier to remember ("sig" can also be "Sigma"), but the keywords ARE
case-sensitive. The "epname" keyword actually has four aliases, "epname",
"atom", "AtomName", and "ExtraPoint." (I went a little overboard there.)

The excl2 keyword is an ATTEMPT at a glaring problem with some extra
points: if they're right on the middle of a bond, or equally close to more
than one real atom in general, how do we count their exclusions? (This is a
reason that one of the experienced force field developers I work with
demands that all of these extra points be close to their ONE parent atom
(which I refer to in mdgx as frame1) to make a tight association.) By
definition, an extra point is 1:1 to its parent atom, so all non-bonded
exclusions of the frame1 atom will be inherited by the extra point. But if
you specify excl2, it's going to take your frame2 atom and say that the
extra point is also 1:1 to that. Ditto for excl3, so the extra point is
accumulating more and more exclusions, atoms that it will not count
interactions with.

This makes me realize that I need to document this part of the code a bit
better, specifically in the onboard manual. There are descriptions for all
mdgx &namelists available by typing, i.e. mdgx -PARAM on the command line.
But not for &rule...

Happy to help more, and you are not the first to make use of mdgx to create
some very unorthodox (not unusual, just not what the typical programs
simulate) molecular models. It HAS been done before, and not just by me :-)


On Fri, May 29, 2020 at 4:30 AM Gao J <> wrote:

> Hello
> I want to perform mix-solvent MD in amber and to prevent aggregation
> ofbenzene probes, I need to set virtual sites on the probes with L-J
> repulsions between themselves merely. My parameters for &rule were as
> follows and I got an error said "ReadEPRuleFile >> Error. Extra point name
> unspecified." So I wonder what the correct format of "epname" or "atom"
> required. What's more, I am a little confused if any parameters needed for
> "excl[1,2]".
> I really appreciate for your help!
> &rule
> frame[1,2]: C1 C4
> epname: VSB
> atom: VSB
> style: 1
> excl[1,2]
> v12: 0.5
> Sig: 21
> eps: 0.01
> residue: UNK
> &end
> _______________________________________________
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Received on Fri May 29 2020 - 03:00:02 PDT
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