[gmx-users] minimum image violation

[Kavyashree M]

Sir,

     I am extremely sorry for this question again :(
but I wanted to know this violation exists only in
first 50ns but after that even though there appears
to be a point of violation its only 1.39nm which is
o0.01nm less than the cut off which I hope does
not cause serious trouble (as the minimum bond
length is of the order of 1 Angs) So can I make use
of this part of trajectory?

     I know that this part of the trajectory have been
arrived at through flawed interactions. But have any one
made such an attempt to analyze this?

Sorry again!

With regards
M. Kavyashree

On Tue, Jun 21, 2011 at 2:46 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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