[gmx-users] Running Grompp in reverse and backing up MD data
Thomas Piggot
t.piggot at soton.ac.uk
Thu Nov 29 17:16:41 CET 2018
Good to know, thanks!
Tom
On 29/11/2018 16:08, Paul bauer wrote:
> 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
>>>>> 340 West Campus Dr.
>>>>> Blacksburg, VA 24061
>>>>>
>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thelemkullab.com&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C84edd7637bf44b1aa1e008d65614ffe9%7C4a5378f929f44d3ebe89669d03ada9d8%7C1&sdata=TVKz0Drugreb7SS3lt%2B9J%2FEUJTWOo8o77n88eyOO%2BQY%3D&reserved=0
>>>>>
>>>>>
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>>>>>
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>
--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
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