You haven't said much about how you actually did these steps, but I can
imagine that making a new (protein trajectory in ascii format with limited
precision could lead to small changes in coordinates and energy
differences.
On Sat, Nov 7, 2020, 8:19 AM Prathit Chatterjee <
prathit.biophysics.gmail.com> wrote:
> Dear AMBER experts,
>
> I had compiled a protein only amber trajectory of an explicitly solvated
> simulation with VMD, which I was able to visualize properly and run certain
> analyses with it in VMD as well.
>
> But, for cross-checking, I tried to calculate the pairwise interaction of
> the protein only generated trajectory (with VMD), and the original AMBER
> coordinates.
>
> The results, although very similar, are showing certain discrepancy as
> follows:
>
> [pchatterjee.node51 pairwise_IE]$ tail -f test*/pairwise_IE.out
> *==> test1/pairwise_IE.out <== [THIS IS THE ORIGINAL AMBER COORDINATE]*
> 1 -186.3642 -2973.0974
> 2 -189.9812 -2966.1259
> 3 -199.5370 -2957.7041
> 4 -196.3846 -2983.7931
> 5 -197.8264 -2981.1530
> 6 -184.0711 -2971.6430
> 7 -194.3659 -2970.1477
> 8 -189.0441 -2956.9308
> 9 -197.0864 -2948.2561
> 10 -196.4939 -3010.1367
>
> *==> test2/pairwise_IE.out <==[THIS IS THE PROTEIN ONLY GENERATED AMBER
> COORIDNATE IN VMD]*
> 1 -186.3943 -2972.9815
> 2 -189.9798 -2966.1573
> 3 -199.5455 -2957.6502
> 4 -196.3961 -2983.7881
> 5 -197.8009 -2981.1609
> 6 -184.0410 -2971.7176
> 7 -194.3681 -2970.0830
> 8 -189.0185 -2956.9181
> 9 -197.1040 -2948.2302
> 10 -196.4685 -3010.0947
>
> Although the global picture will be the same with such minor discrepancy, I
> just want to know for the sake of knowing what the underlying reason could
> be.
>
> Any comments/suggestions will be extremely helpful.
>
> Thank you in advance,
> Best Regards,
> Prathit
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Received on Sat Nov 07 2020 - 07:00:02 PST
