I wonder if the precision of the numbers is the same in both cases? What
format is your mdcrd in? If ASCII, precision is much reduced, otherwise
less of an issue but worth checking by e.g. calcing yourself with the
operations in a different order.
Bill
On 11/7/20 5:19 AM, Prathit Chatterjee 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 - 05:30:02 PST
