[gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  so how come i bring the .gro and newtrj.xtc files in the vmd , my protein doesnt move at all? I think , it is because of the .gro file has protein, ligand and sol cordinates , but the newtrj.xtc has just my protein and ligand. Am i right? 
 

    On Friday, November 10, 2017, 7:20:48 PM GMT+3:30, Justin Lemkul <jalemkul at vt.edu> wrote:  
 
 

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

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