<br>Sir, <br> I would like to thank you for patiently replying for my repeatedly asked question.<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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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.<br>
</blockquote><div> <br>1. protein is not well behaved - This point I dont know how to quantify.<br>2. Box dimensions - I repeated from the model, editconf gave the same box dimensions which I had used earlier but did not <br>
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 <br> 1.4nm.<br>3. I am attaching the mdp file.<br>4. I checked the whole trajectory for change in box size with the output of g_energy. But did not find and abrupt deviations<br>
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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.<br>
</blockquote><div> <br>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<br>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. <br>
<br>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<br>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 <br>
loop would have continued to move without minimum image violation.<br></div><div> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
</blockquote><div><br>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<br>in VMD (which I am not very comfortable with ) and could see a loop movement coming closer to it periodic image. but <br>
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.<br> <br>Thank you for your patience. <br>
<br></div></div>Thank you<br>With Regards<br>M. Kavyashree<br>