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
Received on Wed Sep 28 2011 - 02:30:02 PDT
