Thank you all who responded to my earlier note -- we have the sander api
working for us in a basic sense.
However, we are having trouble reproducing previous results. I suspect
this is because we are comparing a sander_api energy using slightly
different input parameters than our previously-computed sander energy,
which is because the input data structure for the sander_api includes input
parameters that are a modest subset of the total number of sander input
parameters.
Two/three questions related to this:
1) Can I get the sander_api to dump something equivalent to the header in
the mdout file that reports on the values for all of the input parameters?
2) Is it safe for me to assume that it is not too difficult to add a
variable to the sander_api input data structure (e.g. dsum_tol)?
3) And if so, what are all the pieces of code/subroutines that I need to
touch to do this?
Thanks,
Brent
On Tue, May 16, 2017 at 1:52 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > could someone point me to the relevant lines of code that write amber
> topology files?
>
> leap: unitio.c zUnitIOSaveAmberParmFormat
>
> Bill
>
>
> On 5/16/17 9:15 AM, Brent Krueger wrote:
> > Thank you Hai and Dan.
> >
> > My goal was to avoid ever writing the topology file to disk, but it
> sounds
> > like that is not possible. Probably, then, we'll just write the topology
> > file ourselves.
> >
> > I'm sure we can build this from the topology file format definition on
> the
> > amber site, but could someone point me to the relevant lines of code that
> > write amber topology files? Those will surely be a time-saver.
> >
> >
> > Thanks,
> > Brent
> >
> >
> > On Tue, May 16, 2017 at 11:32 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> For now, I think the easiest way is to use sander Python API with
> >> ParmEd's AmberParm. Under the hood, ParmEd save its object to prmtop
> >> file and then passing to pysander.
> >>
> >> https://github.com/Amber-MD/pysander/blob/master/sander/__
> init__.py#L275
> >>
> >> Of couse, we need to build ParmEd's AmberParm (either via tleap or
> >> construct it in memory)
> >>
> >> Hai
> >>
> >> On Tue, May 16, 2017 at 11:03 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >>> Hi,
> >>>
> >>> I don't think passing topology parameters directly is officially
> >>> supported. A brief glance through sander.h shows that there is what
> >>> looks like a topology structure and corresponding function calls:
> >>>
> >>> struct: prmtop_struct
> >>> functions: sander_setup2 (2 versions)
> >>>
> >>> However, they don't appear to be documented or tested, so I would use
> >>> these with extreme caution.
> >>>
> >>> FWIW, cpptraj makes use of the sander API by using the "officially"
> >>> supported method of passing in a topology name. Since this only has to
> >>> be done once the actual overhead is minimal since the topology stays
> >>> in memory after the setup call.
> >>>
> >>> -Dan
> >>>
> >>> On Tue, May 16, 2017 at 9:43 AM, Brent Krueger <kruegerb.hope.edu>
> >> wrote:
> >>>> We would like to use the sander API to do some energy evaluation of
> some
> >>>> simple systems. Part of the goal is to avoid lots of unnecessary disk
> >> I/O.
> >>>> Therefore, we would like to create topology and coordinate information
> >>>> within our own program and keep it resident in memory. The
> coordinates
> >> are
> >>>> easy enough, but I don't see anything in the manual about what data
> >>>> structure holds the topology information and how we can access it.
> All
> >> of
> >>>> the examples simply use the sander_setup_mm() function to read a
> >> topology
> >>>> file from disk.
> >>>>
> >>>> Maybe there are too many idiosyncrasies in the topology construction
> >> and we
> >>>> should just go ahead and use leap or parmed to do that. But our
> >> situation
> >>>> is very simple, We are modeling a crystal lattice, so there are no
> bonds
> >>>> just some ions with VDW parameters and charges. I feel like this is
> >> simple
> >>>> enough that we ought to be able to create this ourselves and pass it
> to
> >> the
> >>>> sander API.
> >>>>
> >>>> Any information or examples would be appreciated. Oh, and we are
> using
> >> C,
> >>>> but I suppose we could use anything else if that would make life
> easier.
> >>>>
> >>>>
> >>>> Thanks,
> >>>> Brent
> >>>>
> >>>> --
> >>>> _______________________________________________
> >>>> Brent P. Krueger.....................phone: 616 395 7629
> >>>> Professor.................................fax: 616 395 7118
> >>>> Hope College..........................Schaap Hall 2120
> >>>> Department of Chemistry
> >>>> Holland, MI 49423
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>> --
> >>> -------------------------
> >>> Daniel R. Roe
> >>> Laboratory of Computational Biology
> >>> National Institutes of Health, NHLBI
> >>> 5635 Fishers Ln, Rm T900
> >>> Rockville MD, 20852
> >>> https://www.lobos.nih.gov/lcb
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor.................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Mon May 22 2017 - 08:00:03 PDT
