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

Fri Jan 13 15:35:17 CET 2017

When I do that it still reads from the beginning, saying “skipping frame”. I’ll divide the file in a few pieces and save all configurations. I’ll then cat the configs that I want. This is the simplest thing I can think of.

> On Jan 13, 2017, at 3:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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
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