[gmx-users] RE: Is non-linear data output/storage possible?

[Justin Lemkul]

On Tue, Jul 2, 2013 at 12:46 PM, Neha <nshafique at wesleyan.edu> wrote:

> So I tried doing this and ran into another problem.
>
> I made two mdp files, one that stored data every ten steps and one every
> hundred steps
>
> I was thinking I would store data like this:
>
> 10
> 20
> 30
> .
> .
> .
> 100
> 200
> .
> .
> .
> 1000
>
> And then I would start another 'block' that would go
>
> 1010
> 1020
> .
> .
> .
> 1100
> 1200
> .
> .
> .
> 2000
>
> I am able to get one block of data stored the way I want. However when I
> use
> grompp to extend the simulation from that block using the mdp file that
> would store data every 10 time steps once again, I get a warning that the
> run will generate an obscene amount of data and that the simulation is
> running for infinite ps. I am not sure why that is happening and was
> wondering if anyone had any ideas as to how to fix it. Or better yet, if
> someone else has a way to do this kind of non-linear data storage that has
> not occurred to me yet.
>
> Let me know if you need anymore information, I understand that this might
> be
> confusing to follow.
>
>
Actual copied and pasted commands, along with full .mdp files (or links to
where they can be downloaded) would help a lot.  With what we have on hand,
all I could tell you is that something is wrong with your .mdp file(s).

-Justin


>
> Dallas Warren wrote
> > Easiest, naïve way that I can see is to do the simulation in blocks, and
> > change the output settings within the mdp file used as required for each
> > block.
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Discovery Biology
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
>
> > dallas.warren@
>
> > +61 3 9903 9304
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble
> a
> > nail.
> >
> >
> >> -----Original Message-----
> >> From:
>
> > gmx-users-bounces@
>
> >  [mailto:gmx-users-
> >>
>
> > bounces@
>
> > ] On Behalf Of Neha
> >> Sent: Thursday, 6 June 2013 11:00 PM
> >> To:
>
> > gmx-users@
>
> >> Subject: [gmx-users] Is non-linear data output/storage possible?
> >>
> >> Hi everybody!
> >>
> >> This is a sort-of general question that I am not sure where to find the
> >> answer for. I am running a simulation on the order of tens of
> >> microseconds.
> >> However I also want to do some analysis on the order of very small time
> >> steps but I do not want to save the data of very small time steps
> >> throughout
> >> the length of the simulation as it will be taxing for the memory. I was
> >> wondering if there was a way to be able to store small time steps for a
> >> small time during the simulation and continue to increase the amount of
> >> time
> >> that energy/forces/coordinates are written and stored?
> >>
> >> I understand the mdp files control the output, but I do not know how to
> >> have
> >> a non-linear output of data using nstxout etc. Please let me know if
> >> you
> >> have any ideas/have succeeded in getting Gromacs to do this!
> >>
> >>
> >>
> >> --
> >> View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-
> >> linear-data-output-storage-possible-tp5008858.html
> >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> >> --
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> View this message in context:
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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-- 

==========================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


==========================================