[gmx-users] extracting a list of frames from a trajectory

[Justin Lemkul]

On 1/13/17 9:15 AM, Irem Altan wrote:
> I need to sample with logarithmic time intervals.
>

Use -b to speed up moving through the trajectory before dumping the desired time 
frame, or split the massive trajectory into smaller, more manageable chunks that 
you can loop over simultaneously.

-Justin

> On Jan 13, 2017, at 3:12 PM, David van der Spoel <spoel at xray.bmc.uu.se<mailto:spoel at xray.bmc.uu.se>> wrote:
>
> On 13/01/17 14:41, Irem Altan wrote:
> Hi,
>
> So for some reason, the frame numbers I list won't match the timestamps when I use -fr. Is there a way to extract frames based on timestamps? The problem is, I want to be reading the file only once (or a few times), as it is huge (~500 GB), so I can’t use -dump by calling trjconv hundreds of times.
>
> How about the -dt flag?
>
> Best,
> Irem
>
> On Jan 13, 2017, at 2:31 PM, Mark Abraham <mark.j.abraham at gmail.com<mailto:mark.j.abraham at gmail.com>> wrote:
>
> Hi,
>
> Sadly there's nothing to be done except ignore the field or do multiple
> passes. The history of trjconv is a large number of people adding features
> convenient for their use case, and not knowing how it interacts with the
> huge surface area of the set of all other features. So the person who
> wanted such automatic regularisation trips the implementation of -fr, etc.
>
> Mark
>
> On Fri, 13 Jan 2017 14:22 Irem Altan <irem.altan at duke.edu<mailto:irem.altan at duke.edu>> wrote:
>
> Hi,
>
> I’m trying to extract a list of frames from a long trajectory:
>
> gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
> atom -o conf_test.gro -sep
>
> where frames.ndx contains the following:
>
> [ frames ]
> 2 3 4 5 6 8 ...
>
> Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
> 20.0000. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
> in water t=  20.00000”, which is what we expect. However, the timestamps in
> the subsequent files are:
>
> Generated by trjconv : Protein in water t=  30.00000
> Generated by trjconv : Protein in water t=  40.00000
> Generated by trjconv : Protein in water t=  50.00000
> Generated by trjconv : Protein in water t=  70.00000
> Generated by trjconv : Protein in water t=  80.00000
> …
>
> while it should have been 30, 40, 50, 60, 80, .... This happens a lot of
> times throughout the whole list of frames. Why does it happen? How can I
> fix it?
>
> Best,
> Irem
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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