On 7/18/12 8:24 AM, nikhil gadewal wrote:
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.
It sounds like you have massive changes to your box dimensions. Since g_hbond
uses a grid-based search scheme to look for hydrogen bonds, such large changes
cause the program to fail.
Investigate the integrity of your .xtc file with gmxcheck and plot box vectors
from the .edr file. Your system may have had serious problems at some point or
the .xtc file became corrupted.
-Justin
*****************************************************************
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.
*********************************************************************
NIKHIL S. GADEWAL
ACTREC,
Tata Memorial Centre,
Kharghar,
Navi Mumbai,
India
--
========================================
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
========================================
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