[gmx-users] vacuum simulation problem with pdb file

[Justin Lemkul]

On 10/5/12 10:16 AM, Paula Andrea Delgado Pinzon wrote:
> Hi all,
> I am trying to do a vacuum simulation with distance restrain, first i did an EM without distance restrastraints, later i did 100 ps to stabilized the T at 300 K but i get this in the pdb file
> ATOM      1  N   MET     1         nan     nan     nan  1.00  0.00
> ATOM      2  H1  MET     1         nan     nan     nan  1.00  0.00
> ATOM      3  H2  MET     1         nan     nan     nan  1.00  0.00
> ATOM      4  CA  MET     1         nan     nan     nan  1.00  0.00
> ATOM      5  CB  MET     1         nan     nan     nan  1.00  0.00
> ATOM      6  CG  MET     1         nan     nan     nan  1.00  0.00
> ATOM      7  SD  MET     1         nan     nan     nan  1.00  0.00
> ATOM      8  CE  MET     1         nan     nan     nan  1.00  0.00
> ATOM      9  C   MET     1         nan     nan     nan  1.00  0.00
> ATOM     10  O   MET     1         nan     nan     nan  1.00  0.00
> ATOM     11  N   THR     2         nan     nan     nan  1.00  0.00
> ATOM     12  H   THR     2         nan     nan     nan  1.00  0.00
> ATOM     13  CA  THR     2         nan     nan     nan  1.00  0.00
> ATOM     14  CB  THR     2         nan     nan     nan  1.00  0.00
> ATOM     15  OG1 THR     2         nan     nan     nan  1.00  0.00
> ATOM     16  HG1 THR     2         nan     nan     nan  1.00  0.00
> ATOM     17  CG2 THR     2         nan     nan     nan  1.00  0.00
>
> Besides it creates several pdb files call step#b_n#.pdb that seems to contain coordinates of some atoms in each file.
>

That means your simulation blew up.  The "nan" refers to "not a number" and is 
printed when the values are infinite.

-Justin

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

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

========================================