Ryan,
Most users are using idecomp 1 or 2 for PB since pairwise reaction
field energies are not well defined in PB. This is different from GB.
If you insist in getting pairwise-decomposed PB energies, I don't
think you can get these with a single PB run for each snapshot.
Nevertheless, the piece of code for idecomp=3 is indeed inside sander,
but it's not tested as it stands. We'll take a look of its behavior
with your files if you don't mind sharing with us. A few snapshots
will do. Please email us off the list.
Ray
On Thu, Sep 5, 2013 at 4:17 PM, Ryan Pavlovicz <pavlovicz.7.osu.edu> wrote:
> Hi,
>
> I recently performed a set of MMPBSA calculations with MMPBSA.py.MPI
> (AmberTools 13, patches update.1-update.14 applied) using idecomp=1 with
> good results. I then attempted to perform a pair-wise decomposition on the
> same data set using idecomp=3 and noticed inconsistent EPB results.
>
> The -o output (which i wouldn't expect to be affected by the idecomp
> setting) was nearly identical for all components of the two calculations
> except for the EPB values.
>
> Here are the input parameters:
>
> INPUT1:
>
> &general
> endframe=4000, verbose=2, keep_files=2, debug_printlevel=2,
> /
> &pb
> istrng=0.150, inp=1, cavity_offset=0.92, cavity_surften=0.00542,
> /
> &decomp
> idecomp=1, print_res="1-257"
> dec_verbose=1,
> /
>
> INPUT2:
>
> &general
> startframe=1, endframe=4000, verbose=2, keep_files=2, debug_printlevel=2,
> /
> &pb
> istrng=0.150, inp=1, cavity_offset=0.92, cavity_surften=0.00542,
> /
> &decomp
> idecomp=3, print_res="58,61-62,65-66,69,74-75,79-84,86-87,92,232-257"
> dec_verbose=1,
> /
>
> And some of the -o output averages for the complex energies:
>
> from INPUT1 calculation:
>
> BOND 767.3825
> ANGLE 2123.0202
> DIHED 1591.6132
> VDWAALS -2048.7067
> EEL -17663.9213
> 1-4 VDW 956.6694
> 1-4 EEL 9456.6797
> EPB -2936.0288
> ENPOLAR 71.5819
>
> form INPUT2 calculation:
>
> BOND 767.3857
> ANGLE 2123.0294
> DIHED 1591.6116
> VDWAALS -2048.7072
> EEL -17663.9226
> 1-4 VDW 956.6795
> 1-4 EEL 9456.6795
> EPB -1.6261
> ENPOLAR 71.5807
>
> In all five sets of calculation i performed, the EPB values for the
> idecomp=3 simulations were very small compared to those obtained from the
> idecomp=1 simulations. Maybe someone can spot an error in my inputs or
> identify this as a bug in the MMPBSA.py code.
>
> If this is a bug, i assume that the pair-wise Polar Solvation terms may
> also not be correct. They all seem fairly small in my -do files (ranging
> from about -1 to 1), although i'm not sure how small they should be when
> broken down pair-wise.
>
> Any help would be much appreciated.
>
> Thanks,
>
> ryan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 06 2013 - 11:30:04 PDT
