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 
<sp...@xray.bmc.uu.se<mailto:sp...@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.abra...@gmail.com<mailto:mark.j.abra...@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.al...@duke.edu<mailto:irem.al...@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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