[gmx-users] Periodic Images - clarification

[Kavyashree M]

Sir,
 I would like to thank you for patiently replying for my repeatedly asked
question.

>
> 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.
>

1. protein is not well behaved - This point I dont know how to quantify.
2. Box dimensions - I repeated from the model, editconf gave the same box
dimensions which I had used earlier but did not
    repeat the NVT. and the distance -d between wall of box and protein atom
was kept as 1.0nm while the max cut of used was
   1.4nm.
3. I am attaching the mdp file.
4. I checked the whole trajectory for change in box size with the output of
g_energy. But did not find and abrupt deviations


> 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.
>

I did not anticipate such a violation would as it did not happen in other
cases. so I did not check the minimum image violation
while running the simulation but caculated after 100ns. I agree it was my
stupidity. Because of time constraints and system unavailability now I might
not be able to run another simulation. But I will be running it later with
corrected parameters for sure.

I agree that it is producing flawed results. But My point was if at all it
was caused only due to the box dimension being smaller
and not due to any wrong parameters used why is that 26ns wrong. Probably if
I had selected a bigger box size may be that
loop would have continued to move without minimum image violation.


> 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.
>

If I am running again I would increase the box size and run. I did what you
had suggested.  I visualized that part of trajectory
in VMD (which I am not very comfortable with ) and could see a loop movement
coming closer to it periodic image. but
unfortunately because of my lack of know-how I was unable to measure the
distance between them in VMD. I could only visualixe the loop movement but I
am unable to produce and concrete outputs for my observation.

Thank you for your patience.

Thank you
With Regards
M. Kavyashree
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