[gmx-users] Re: Extracting the timestep value from topology and/or trajectory files

[Reid Van Lehn]

Check gmx_energy.c. It contains this line:

read_tpx(topnm, &ir, box, &natoms, NULL,NULL, NULL, &mtop);

where ir is t_inputrec.

Reid

On Thu, Feb 21, 2013 at 1:48 PM, shavit <shavit at seas.upenn.edu> wrote:

> I think your'e right.  I'm currently trying to make it work, but am not
> really succeeding.  I'm declaring t_inputrec *ir, and then trying to
> reference ir->delta_t.  Even in compile-time, I get a warning that delta_t
> is being used without being initialized, which makes sense.  Is there any
> function that is called in the standard gromacs template that initializes
> and sets delta_t to the timestep size?
>
> My apologies if this is a beginner's question, and thank you so much for
> your help,
>
> Amit
>
>
> On Thu, Feb 21, 2013 at 1:11 PM, Justin Lemkul [via GROMACS] <
> ml-node+s5086n5005770h71 at n6.nabble.com> wrote:
>
> >
> >
> > On 2/21/13 9:47 AM, shavit wrote:
> >
> > > Hello,
> > >
> > > For several months now, I've been writing my own analysis tools using
> > the
> > > GROMACS template.c file.  There is one thing I haven't been able to
> > figure
> > > out, and that is how to get the timestep size.
> > >
> > > I'm confident this parameter is located in either the traj.trr file or
> > the
> > > topol.tpr that I feed into all of my analysis codes, I just can't
> figure
> > out
> > > how to access it.
> > >
> >
> > If memory serves, the t_inputrec structure holds it in ir->delta_t.
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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-- 
Reid Van Lehn
NSF/MIT Presidential Fellow
Alfredo Alexander-Katz Research Group
Ph.D Candidate - Materials Science