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
