It is not obvious to me that per-residue (or pairwise per-residue) energy
contributions are accumulated in the periodic electrostatic routines (I
know they work for GB). If your energies are coming out to be zero, my
guess is that these non-bonded terms are not accumulated for ntb>0.
Another thing to be wary of is that decomposition results for PME would be
*completely* arbitrary with respect to your cutoff. And unlike GB
calculations, you cannot use an 'infinite' cutoff.
In PME, the direct and reciprocal space terms are interdependent.
Specifically, the width of the neutralizing Gaussian counterion dictates
how long-range the direct space portion of the calculation is (and,
ultimately, how large your cutoff should be) and how many terms to include
in your reciprocal space sum (the shorter the cutoff, the narrower the
Gaussians, the shorter-range the direct space term is and the more terms
that are in the reciprocal space sum).
While the direct-space sum is pairwise decomposable, the reciprocal space
part (computed using an FFT) is definitely not, and Amber has no way to
even approximately decompose it.
HTH,
Jason
On Wed, Sep 19, 2012 at 10:49 PM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber developers and users,
>
> I am so sorry to send similar question
> again.
>
> I am trying to recalculate energy from
> an obtained MD trajectory,
> Where IDECOMP = 1 and NTB = 1.
>
> To confirm the available MD input,
> I changed the input file in
> ~/amber12/test/trajene_box,
> But it does not work.
>
> Total energy was calculated but the
> decomposition was not printed, properly.
>
> I will show both of input files;
> original one and modified one.
> I am most grateful if you give me some
> advice to improve this situation,
> Or would you let me know that Amber12
> does not work in this situation, if so.
>
> Sincerely yours,
>
>
> Kurisaki
>
>
> >Original Input files:
>
> TIP3P PP
> &cntrl
> imin = 5, ntx = 1, irest = 0,
> ntt = 1, tautp = 1.0, temp0 = 300.0,
> tempi = 300.0,
> ntc = 2, ntf = 1, ntb = 2,
> ntp = 1, taup = 1.0,
> ntwx = 10, ntwe = 0, ntwr = 10, ntpr
> = 10, ioutfm = 0,
> cut = 8.0, iwrap = 1,
> &end
>
>
> >Modified one:
> TIP3P PP
> &cntrl
> imin = 5, ntx = 1, irest = 0,
> ntt = 1, tautp = 1.0, temp0 = 300.0,
> tempi = 300.0,
> ntc = 2, ntf = 1, ntb = 1,
> ntwx = 10, ntwe = 0, ntwr = 10, ntpr
> = 10, ioutfm = 0,
> cut = 8.0, iwrap = 1,
> idecomp = 1,
> /
> Residues considered as REC
> RRES 1 2
> END
> Residues considered as LIG
> LRES 3 4
> END
> Residues to print
> RES 1 4
> END
> END
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 19 2012 - 20:30:02 PDT
