[gmx-users] Running Grompp in reverse and backing up MD data
Thomas Piggot
t.piggot at soton.ac.uk
Thu Nov 29 17:00:25 CET 2018
You can get an mdp from a tpr using gmx dump -om
Cheers
Tom
On 29/11/2018 14:58, Peter Kroon wrote:
> Hi all,
>
>
> thanks for all the feedback.
>
> @Milan: I've made a tally of diskspace used per filetype in our lab. In
> general people here don't save trr files at all (too expensive), yet
> still out of 125TB total, 65% is made up of xtc files, and 10% is trr
> files (followed by gro and xvg at 2.5% each). And that kind of backup
> space becomes expensive. Of course for some simulations that were super
> expensive to run we should back up the trajectories. But as a general
> solution it's impossible. That also opens up the point of tiered
> backups. For example: archive for the past 5 years to verify old
> research results; off-site backups for the past 3 months in case the
> building burns down; and local storage against accidental deletion. For
> each there are different requirements and costs.
>
> @Mark: Part of the reason for this discussion is figuring out what my
> responsibility is exactly. My thought was that as the TPR in general
> contains the same information as the input used to make it, at least a
> partial reverse should be possible. Then again, mdp/top/itp files are
> pretty small (17GB/35GB/110GB respectively) and should be very
> compressible. By comparison, tprs make up 880GB here.
>
> @Justin: Great point, thanks!
>
>
> Thanks guys :)
>
>
> Peter
>
>
> On 29-11-18 15:29, Mark Abraham wrote:
>> 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
>>>
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>>>
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--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
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