Dear Jason,
I can prepare an available input file from test directory,
And I got proper results for my interesting system.
The Input file is below:
#decompose energy on a per-residue basis on the trajectory
&cntrl
imin = 5, igb = 5, gbsa = 2,
ntx = 1, maxcyc = 1,
ntc = 2, ntf = 2,
ntb = 0, ntp = 0,
ntwe = 0, ntpr = 500, ntwx=1,
cut = 1000.0, idecomp = 1,
/
Residues considered as REC
RRES 1 13
END
Residues considered as LIG
LRES 1 13
END
Residues to print
RES 1 13
END
END
Here, all water molecules were striped from crd and mdcrd files.
However, when I turned igb frag to 0,
Calculateions cannot proceed.
There is another question related to initial one.
When I ask you, I used crd and mdcrd files with Explicite Water Molecules
With NTB=1 and IGB=0.
Does IDECOMP frag can work only when IGB > 0?
Thank you for your kind support.
Ikuo KURISAKi
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Wednesday, September 28, 2011 9:58 PM
To: AMBER Mailing List
Subject: Re: [AMBER] sander outout using mdin=5 and idecomp=2
What version of Amber are you using?
On Wed, Sep 28, 2011 at 5:13 AM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber users and developers,
>
>
>
> Thank you for usual support.
>
>
>
> I am trying to calculate energy by residue
>
> >From obtained MD trajectories.
>
>
>
> MDIN = 5 and IDECOMP = 2 are set in sander input file.
>
> The calculations were done, energy terms were decomposed,
>
> However, output data seems slight strange as shown below.
>
>
>
> First, conventional energy output:
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
> 1 -1.2939E+05 1.9485E+01 1.2163E+02 CE2 2985
>
>
>
> BOND = 891.0085 ANGLE = 2373.6767 DIHED =
> 3040.4776
>
> VDWAALS = 19786.0597 EEL = -167848.7590 HBOND =
> 0.0000
>
> 1-4 VDW = 1033.4558 1-4 EEL = 11335.9261 RESTRAINT =
> 0.0000
>
>
>
> Next, decomposed energy output:
>
>
>
> PRINT DECOMP - TOTAL ENERGIES
>
>
>
> resid |internal |vdw |eel |pol |sas
>
> ============================================================
>
> TDC 1 10.249 0.000 0.000 0.000 0.000
>
> TDC 2 22.599 0.000 0.000 0.000 0.000
>
> TDC 3 9.283 0.000 0.000 0.000 0.000
>
> TDC 4 15.083 0.000 0.000 0.000 0.000
>
> TDC 5 10.258 0.000 0.000 0.000 0.000
>
>
>
>
>
> I found vdw and eel energies were not printed out in decomposition.
>
> I am most grateful if you give me some advices for this case.
>
>
>
> Sincerely yours,
>
>
>
> Ikuo Kurisaki
>
>
>
> PS
>
>
> I used following input file.
>
>
>
> &cntrl
>
> TIMLIM = 999999, IMIN = 5,
>
> MAXCYC=0,
>
>
>
> NTX = 1, IREST = 0, NTRX = 1,
>
>
>
> NTXO = 1, NTPR = 500, NTWR = 500, IWRAP = 0,
>
> NTWX = 0,
>
>
>
> IDECOMP = 1,
>
>
>
> NTF = 2, NTB = 1,
>
> CUT = 9.0,
>
>
>
> NTC = 2, TOL = 0.000001,
>
>
>
> /
>
> &end
>
> Residues
>
> RRES 1 5
>
> END
>
> REResidues
>
> RES 1 5
>
> 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 28 2011 - 07:30:02 PDT
