[gmx-users] Running Grompp in reverse and backing up MD data
Paul bauer
paul.bauer.q at gmail.com
Thu Nov 29 17:08:05 CET 2018
Hello,
just a warning concerning the last message: The mdp from gmx dump -om
will not be the complete representation of your tpr, and you will not be
able to regenerate the tpr from this mdp file! I have been working on a
variant that would make this possible, but so far have not managed it.
Cheers
Paul
On 29/11/2018 16:53, Thomas Piggot wrote:
> 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
>>>>
>>>> Virginia Tech Department of Biochemistry
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>>>>
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>
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