[gmx-users] Missing frames in trajectory?

[Justin Lemkul]

On Tue, Jul 2, 2013 at 7:26 AM, Humphrey Morhenn <
Humphrey.Morhenn at frm2.tum.de> wrote:

> Dear users,
>
> there seem to be alot of frames missing in my .trr trajectory file and I
> wonder if anyone knows how to recover the (hopefully not lost) information.
>
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 120000000
> nstxout                  = 1000000
>
> When I e.g. run trjconv -pbc mol -f (.trr) -s (.tpr) -o (.trr), it says:
> Reading frame  0 time 77000.000
> Reading frame 30 time 107000.000 -> frame 30 time 107000.000
>
> What happened to the frames <77ns and >107ns?
>
>
When running trjconv, trjcat, etc, Gromacs reports the frame it is reading
and then over-writes the line as it progresses through the trajectory. You
have 30 frames spanning 30 ns, which is exactly what your .mdp file
specifies.  You haven't posted any information (previous protocol,
remainder of .mdp, etc) that would indicate why the trajectory starts at 77
ns.

-Justin

-- 

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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


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