[gmx-users] Running Grompp in reverse and backing up MD data

[Mark Abraham]

Hi,

Yes, that's useful output, though strictly some mdp settings (like
constraints and gen-vel) are consumed by grompp and thus not reported there.

Mark

On Thu, Nov 29, 2018 at 3:16 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/29/18 6:43 AM, Peter Kroon wrote:
> > Hi Mark,
> >
> > thanks for the rapid reply!
> >
> > Hmmn. It doesn't have to be exactly matching input. An equivalent to
> > e.g. mdout.mdp produced by grompp would already be good enough for my
>
> All of the input .mdp settings are also written to the header of the
> .log file for the run.
>
> -Justin
>
> > purposes. The same goes for a top file containing only the interactions
> > relevant to the system.
> >
> >
> > Peter
> >
> > On 29-11-18 11:31, Mark Abraham wrote:
> >> Hi,
> >>
> >> Unfortunately there is no way to generate matching inputs to grompp
> from a
> >> .tpr file. In the longer term, we want that to be possible, but it will
> >> require a total rework of how users specify inputs, and that's a large
> >> effort!
> >>
> >> Mark
> >>
> >> On Thu, Nov 29, 2018 at 11:27 AM Peter Kroon <p.c.kroon at rug.nl> wrote:
> >>
> >>> Hi all,
> >>>
> >>>
> >>> In the lab we're thinking about backup solutions for MD data (and in
> >>> particular gromacs produced data). Since trajectories tend to be large
> >>> we quickly decided that backing up the results of simulations is a
> waste
> >>> of disk space. Instead, we'll probably go for backing up the TPR files.
> >>>
> >>> Now for the question: Is there an easy way of generating the files used
> >>> to generate the TPR files? For example the MDP file used to make a TPR
> >>> file? How about a top file (I assume the original split between top and
> >>> itp is lost)? I know I can get the starting configuration (gro) using
> >>> editconf.
> >>>
> >>> And does anyone here have any other blinding insights on backing up MD
> >>> data?
> >>>
> >>>
> >>> Cheers,
> >>>
> >>> Peter
> >>>
> >>>
> >>> --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
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