I would extend the simulation upto 20 ns if possible.
I would then extract 10-20 sps for each ns of MD and run MMPBSA for each ns to see if energies converge roughly between 10 to 20 ns.
Good luck!
Jenk
________________________________
From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, February 14, 2012 12:04 PM
Subject: Re: [AMBER] MMPBSA results and huge SD
I took 100 sps, from the las 1ns of my MD simulation.
I have checked the RMSD and energies and based on that system was stable, thus I decided to run MMPBSA.
/Urszula
________________________________________
Von: mish [smncbr.gmail.com]
Gesendet: Dienstag, 14. Februar 2012 10:26
An: AMBER Mailing List
Betreff: Re: [AMBER] MMPBSA results and huge SD
What do you mean by "I run MMPBSA calculations for a protein-peptide
complex for 100 sps" ? What I can think of is ..you take snapshots at each
100ps from a 10ns long MD simulation of the complex. Best would be to
choose the last few ns of your MD simulation where your system had stable
dynamics. Have a look in the backbone RMSD of protein and also in the
energies so that you can decide what part of your MD simulation is not
stable and need to be excluded from the calculations.
Hope it helps.
Sincerely
Mish
On Tue, Feb 14, 2012 at 10:14 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
>
> Dear Amber users,
>
> I run MMPBSA calculations for a protein-peptide complex for 100 sps. The
> MD simulations were carried out for 10ns, complex was stable...
> below I pasted the results that I received from mmpbsa run, what I dont
> understand is this huge STD value ... ? why is that? where does it come
> from?
> I have also checked the single sps and rerun MMPBSA, however I have not
> seen such as big deviation.
> How should I understand PBTOT= -129.74 with STD=75.51?
>
>
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -322.09 138.62
> VDW -86.14 39.01
> INT 0.00 71.77
> GAS -408.23 152.07
> PBSUR -80.64 9.24
> PBCAL 359.13 122.81
> PBSOL 278.49 119.83
> PBELE 37.04 50.97
> PBTOT -129.74 75.51
> GBSUR -13.50 1.53
> GB 447.06 132.54
> GBSOL 433.56 132.07
> GBELE 124.97 86.27
> GBTOT 25.33 109.88
>
>
> Thank you in advance for any comments,
>
> best regards
> Urszula
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 14 2012 - 08:00:02 PST
