Not urgent, but I'm hoping to get it in and tested for Amber14. The code
(soon to be committed) as it is now works for any LES topologies that ptraj
works for; I just wanted to make sure I wasn't missing something obvious.
-Dan
On Tue, Dec 3, 2013 at 5:26 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Well this is me, since I wrote all of that code. I'm really overloaded
> already this week so I hope it isn't urgent....
> On Dec 3, 2013 6:50 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>
> > Hi All,
> >
> > I've been adding LES trajectory splitting/averaging to cpptraj and have
> hit
> > a snag. Everything works fine if I'm using a "simple" LES topology
> > (something like copies of only one region). However, if I try to make a
> > more complex LES topology (varying #s of copies of several regions) I
> get a
> > topology that's not set up the way I had expected (details below). This
> is
> > probably just a case of me not understanding how an LES topology is set
> up,
> > so before I get into the details of my problem I was wondering are LES
> > topologies are described in-depth anywhere? I searched through the
> website
> > and GIT tree docs but was unable to find anything.
> >
> > This is what I currently understand the LES-related flags in the topology
> > to mean:
> >
> > LES_NTYP: Total number of LES types.
> > LES_TYPE: LES type for each atom
> > LES_FAC: LES scaling factor for interaction of typeA x typeB (essentially
> > an NTYP*NTYP matrix)
> > LES_CNUM: LES copy # for each atom
> > LES_ID: LES region ID, corresponding to the original 'spac' entries in
> > addles input
> >
> > The stuff that's important for LES trajectory splitting is LES_CNUM; an
> > atom has CNUM of 0 if its in every copy, otherwise the CNUM is what copy
> > that atom belongs to. So what makes sense is that the number of 0 entries
> > plus the number of any individual copy should equal the total number of
> > atoms in the original (non-LES) topology. This seems to be the case for
> an
> > LES topology with input like this:
> >
> > ~ 3 copies of the fragment consisting of residues 191 to 215
> > spac numc=3 pick #mon 191 215 done
> >
> > But not for an LES topology with input like this:
> >
> > ~ 3 copies of the fragment consisting of residues 191 to 215
> > spac numc=3 pick #mon 191 215 done
> > ~ 4 copies of the fragment consisting of residues 234 to 243
> > spac numc=4 pick #mon 234 243 done
> > ~ 2 copies of the fragment consisting of residues 42 to 55
> > spac numc=2 pick #mon 42 55 done
> > ~ 3 copies of the fragment consisting of residues 55 to 60
> > spac numc=3 pick #mon 55 60 done
> >
> > The latter input has CNUM entries that go up to 6; however the total for
> > each copy does not add up to the # of atoms in the original topology (in
> > this case 4049). This is how CNUM breaks down:
> >
> > CNUM: #_of_atoms_with_that_cnum Total
> > 0: 3232
> > 1: 817 4049
> > 2: 817 4049
> > 3: 594 3826
> > 4: 140 3372
> > 5: 14 3246
> > 6: 14 3246
> >
> > The first two appear fine, but after that its strange. Note that the
> > ordering of the 'spac' entries doesn't appear to affect CNUM, but does
> > appear to affect the last number in POINTERS (NCOPIES I think?), which
> BTW
> > never equals 6.
> >
> > Any ideas?
> >
> > -Dan
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Dec 03 2013 - 17:00:02 PST
