VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Nov 07 2020 - 19:35:23 CST

Dear Prathit,
We really need more information on how you did these calculations. How were
the energies calculated? And how exactly did you generate the trajectory in
vmd? With such small differences it could be something as simple as a
difference in the numerical precision at which coordinates were stored,
depending on exactly what formats you used.
Best,
Peter

On Sat, Nov 7, 2020 at 10:02 AM Prathit Chatterjee <
pc20apr_at_remove_yahoo.co.in> wrote:

> Dear VMD 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
> original AMBER coordinates, and the protein only generated trajectory
> (with VMD).
>
> The results, although very similar, are showing certain discrepancy as
> follows:
>
> [pchatterjee_at_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
>
>