[gmx-users] SD error

[Wei Fu]

Hi, all,

    Has anybody have experience on analysis of stochastic dynamics tryjectory. I performed SD simulation on four systems, but I found when I use "trjconv" convert trajectory to pdb file, the strange pdb coordinates were generated for all four systems.

When simulation runs to 10ps, the coordinate looks OK, but when simulation runs to 40ps for first system, the coordinates are as follows:

_____________________________________________________________
ATOM      1  N   ASN     1         nan     nan     nan  1.00  0.00
ATOM      2  H1  ASN     1         nan     nan     nan  1.00  0.00
ATOM      3  H2  ASN     1         nan     nan     nan  1.00  0.00
ATOM      4  H3  ASN     1         nan     nan     nan  1.00  0.00
ATOM      5  CA  ASN     1         nan     nan     nan  1.00  0.00
ATOM      6  CB  ASN     1         nan     nan     nan  1.00  0.00
ATOM      7  CG  ASN     1         nan     nan     nan  1.00  0.00
ATOM      8  OD1 ASN     1         nan     nan     nan  1.00  0.00
_____________________________________________________________

   For other three systems, when they run to different time, for example, when it runs to 400ps for the second system, the following coordinate was generated. And the SD still run further, no any warning, no step*.pdb files were generated. I do not know what is the problem, how to solve it?

   Any hints were highly appreciated!

Linda

2004-02-10
************************************************************
  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry 
  University of Houston
  4800 Calhoun Rd. HSC #402C
  Houston, TX 77204-5001   USA
  Phone:713-743-8355(o)  713-795-9270(h) 
  Fax:713-743-8351 
  Email: fuwei at adrik.bchs.uh.edu
  http://adrik.bchs.uh.edu/~fuwei/
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