[gmx-users] printing coordinates using template.c

[Justin A. Lemkul]

Chandan Choudhury wrote:
> Hello gmx users !!
> 
> I was trying to use template.c. There I printed out the coordinates of a 
> trajectory file using the printf statement as under:
> 
> printf("Coordinates at t=%8.3f : %8.5f %8.5f 
> %8.5f\n",fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]);
> 
> 
> The output was
> Reading frame     100 time 4400.000   Coordinates at t=4400.000 :  
> 9.34053  4.26640  8.23887
> 
> 
> 
> This is the output of the 4400.000 th time or 100th frame of the first 
> Atom in the trr file.
> 
> Secondly, I dumped the 100th frame using tpbconv (of the same trajectory 
> as above) as:
> trjconv  -s *.tpr -f *.trr  -dump 4400.00 -o frame100.pdb
> 
> The frame100.pdb reads as:
> 
> ATOM      1  N   NGL A   1      93.405  42.664  82.389  1.00  0.00
> ATOM      2  H1  NGL A   1      93.849  42.216  81.599  1.00  0.00
> ATOM      3  H2  NGL A   1      93.914  43.464  82.737  1.00  0.00
> ATOM      4  H3  NGL A   1      93.577  41.958  83.090  1.00  0.00
> ATOM      5  CA  NGL A   1      91.980  42.980  82.205  1.00  0.00
> ATOM      6  HA  NGL A   1      91.538  41.996  82.050  1.00  0.00
> ATOM      7  CB  NGL A   1      91.260  43.708  83.336  1.00  0.00
> ATOM      8  HB1 NGL A   1      90.206  43.782  83.068  1.00  0.00
> ATOM      9  HB2 NGL A   1      91.603  44.742  83.372  1.00  0.00
> 
> 
> We can clearly see the difference in the coordinates of the 1st Atom 
> (ATOM 1 N).
> 
> That is the coordinates produced by the template are different than 
> those of trjconv's.
> 
> Can someone help me out to correctly printf the x, y z coordinate using 
> the template.c file.
> 

Both are correct.  Gromacs tools use nm units, and PDB files use Angstrom.

-Justin

> Thanks
> 
> Chandan
> 
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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