[gmx-users] minimum image violation

[Justin A. Lemkul]

Kavyashree M wrote:
> Dear users,
>  
>     I ran 100ns simulation for 4 proteins, 3 of them were
> non covalent dimers in solution, but only 1 is a covalent
> dimer connected by a disulphide bridge. I used monomers
> to run the job.
>     Only in the case of covalent dimer I was getting severe
> minimum image violation ie. out of 50001 data points,
> 282 are <= 1.4nm
> 280 are < 1.4nm
> 144 are < 1.3nm
> 79 are < 1.2nm
> 28 are < 1.1nm
> 4 < 1.0nm
> 
> I agree that this is quite wrong but I wanted to know whether
> any useful information can be gathered out of this simulation?
>  

Not likely.  Nearly 2% of the saved frames are unusable, indicating that 
potentially even more of the frames in the trajectory are useless, as well, and 
the dynamics that produced them are flawed.

> In another data while calculating the energy terms it gives
> nan (not a number error) for rmsd alone eg -
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Temperature                     300      9e-05       -nan -0.000501989  (K)
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                    0.99914      0.027       -nan  0.0174391  (bar)
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Volume                      517.755     0.0094       -nan   0.010871  (nm^3)
>  
> Initially i though some data points are missing but later
> gmxcheck gives that all the data points are present.
> now what could be the error?
> 
> I had asked this question before and was instructed to check the
> trajectory. I checked the rmsd rmsf of this with the other proteins
> it similar but one of the segment has high rmsf compared to the other
> proteins.
> 

My advice to you was to *watch* the trajectory to see where the PBC violations 
occurred, not run more analysis.  I doubt RMSF and RMSD will tell you anything 
useful.

No one's been able to diagnose the problem based on this (continually posted) 
information.  If it's a useless trajectory, why bother?

-Justin

> Thanking you
> With regards
> M. Kavyashree
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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