[gmx-users] Periodic Images - clarification

[Justin A. Lemkul]

Kavyashree M wrote:
> Dear users,
> 
> I apologize for asking the same question. but I wanted a clarification
> regarding this
> 
> I had done a simulation for 100ns which had minimum image violation
> after 27ns. I have asked this question several times and people have
> suggested me not to use the results. But I just wanted to know if I use
> the frames upto 26ns and do an analysis will it be wrong? and if I report
> that this minimum image violation had occurred.
> 
> Correct me if I am wrong. This minimum image violation occurs only if
> the box size is inadequate. is it right? In the present simulation I had
> made sure that cut off (1.4nm) was much less than the periodic image
> distance 2.0nm. I may just ignore this data and do another simulation,
> But I wanted to know this aspect.
> 

For most stable, well-behaved proteins, setting a suitable box size at the 
outset of the simulation is sufficient to avoid spurious PBC interactions.  In 
your case, there are several possibilities: (1) the protein is not well-behaved, 
(2) you didn't set the box you think you did, (3) the .mdp settings are wrong 
and lead to instability, or (4) your pressure coupling settings cause the box to 
shrink unreasonably.

If you want to use the first 26 ns only, I suppose these data are legitimate, 
although then several questions arise.  Why did you run 100 ns in the first 
place?  Presumably you felt that you needed such a simulation length to address 
whatever question you're asking, so is 26 ns legitimate, or is it simply 
convenient because you don't want to run the simulation again?  Also, why trust 
these results when you know that just a short time later these dynamics produced 
flawed information?  The PBC violation may not have simply happened suddenly; 
maybe it was a product of some long-term motion in the system that was 
continually trending towards disaster.

The biggest question is, if you run the simulation again (which you should, but 
only after answering the four points above and the following), how do you know 
the same thing won't happen again?  You've been asking related questions for 
weeks and I still do not know if you have followed my repeated advice to watch 
the trajectory with a PBC unit cell enabled in your favorite visualization 
program and, in concert with the identified problematic atoms in the g_mindist 
output, identify where and why the minimum image violation occurred.  Doing so 
should take minutes and you should immediately see what went wrong, which would 
be valuable information for avoiding such behavior in the future.  If you have 
done this, you've posted no evidence of your findings and thus just wasted weeks 
posting the same (or tangentially related) questions with no answer, time that 
could have been spent running a proper simulation to recover what you lost.

-Justin

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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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