Dear all,
I am calculating a protein with ab initio method using explicit water
model.But when I minimize the solvent environment energy, I find that the
term of VDWAALS in the min1.out file are very large, which made the
protein disconected.
the min1.in file:
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb=1,
ntr=1,
cut = 12.0
/
Hold the protein fixed
50.0
RES 1 52
END
END
The min1.out file:
--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.2
|
| 01/10/2013
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
BOND = 85.8983 ANGLE = 234.2699 DIHED = 1642.1355
VDWAALS = 34036816.3028 EEL = 71478981.6109 HBOND =
0.0000
1-4 VDW = 284.0258 1-4 EEL = 3914.3180 RESTRAINT =
1.0803
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -6.4148E+09 1.9159E+06 8.3886E+06 HG22 1134
BOND = 3.5674 ANGLE = 211535.9324 DIHED =
4808.5590
VDWAALS = ************* EEL = 139046.2086 HBOND =
0.0000
1-4 VDW = 53056198.9024 1-4 EEL = 20.9546 RESTRAINT =
-0.0000
EAMBER = *************
.... RESTARTED DUE TO LINMIN FAILURE ...
Any help will be appreciated !
Tu
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Received on Sat Apr 06 2013 - 20:30:02 PDT
