[gmx-users] Error reading .xtc file

[Justin Lemkul]

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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