[gmx-users] peptide ligand

[Justin Lemkul]

On 11/10/17 10:35 AM, farial tavakoli wrote:
> Dear Justin
>
> Thank you for replying
>
> This is my input xtc file :
>
> gmx check -f md_0_1.xtc
>
> Checking file md_0_1.xtc
> Reading frame       0 time    0.000
> # Atoms  49582
> Precision 0.001 (nm)
> Last frame       1000 time 10000.000
>
>
> Item        #frames Timestep (ps)
> Step          1001    10
> Time          1001    10
> Lambda           0
> Coords        1001    10
> Velocities       0
> Forces           0
> Box           1001    10
>
> and this is my output xtc file:
>
> gmx check -f newtrj.xtc
>
> Checking file newtrj.xtc
> Reading frame       0 time    0.000
> # Atoms  3378
> Precision 0.001 (nm)
> Last frame       1000 time 10000.000
>
>
> Item        #frames Timestep (ps)
> Step          1001    10
> Time          1001    10
> Lambda           0
> Coords        1001    10
> Velocities       0
> Forces           0
> Box           1001    10
>

These outputs do not support your assertion that newtrj.xtc only 
contains one frame. Clearly both the old and new trajectories have the 
full 1001 frames.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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