It could certainly be reasonable if the two simulations sampled different
regions of phase space. One thing that may help you decide one way or the
other is to do a decomposition analysis and see which residues changed the
most, then take a look at how those specific residues behave throughout the
course of each simulation. That is, of course, if no large-scale
conformational differences between the 2 can be discovered by quickly
comparing the trajectories. Keep in mind that just because 2 structures
have an RMS of 2.5 A from a common structure does not mean that they are
identical themselves.
Good luck!
Jason
On Sun, Jun 13, 2010 at 11:20 AM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> I did a calculation twice, each 10 ns, start with the same prmtop and
> inpcrd files. Both systems comes to a constant ETOT energy after 2ns. RMSD
> less than 2.5A and become stable after 2ns.
>
>
>
> However, I found the results from the two runs are different.
>
>
>
> Then, I do the GBSA analysis. I found the MM/GBSA total energies are
> different by ~6 kcal/mol.
>
>
>
> Could you mind to share your experience with me if it is a reasonable
> results?
>
>
>
> Best regards,
>
>
>
> Cat
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Jun 13 2010 - 10:00:04 PDT
