[gmx-users] Error reading .xtc file

nikhil gadewal ngadewal at yahoo.com
Wed Jul 18 14:24:50 CEST 2012

Dear users,

I am getting the problem in reading full .xtc file. The simulation time is 200 ns. But while giving command

./g_hbond -f dna_pro_whole_nojump_cent.xtc -s sys2.tpr -num Pro_H2A2.xvg

I am getting below error.  The .xtc file is reading only till 20ns and givng error. I am not getting error for other .xtc files

Please provide soultion to the problem.


Calculating hydrogen bonds in Protein (12424 atoms)
Found 1231 donors and 2226 acceptors
Reading frame       0 time    0.000   
Will do grid-seach on 29x20x30 grid, rcut=0.35
Reading frame    2000 time 20000.000   
Program g_hbond, VERSION 4.5.5
Source code file: gmx_hbond.c, line: 1211

Fatal error:
Your computational box has shrunk too much.
g_hbond can not handle this situation, sorry.

Tata Memorial Centre, 
Navi Mumbai,

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