Dear Amber Users,
I have a problem with the Thermodynamic Integration:
I want to mutate an adenine into a thymine (the first and last base from
an 10 base-pair long DNA). And during the
last step, when adding the charges to the thymine at the lambda steps
0.1, 0.3 and 0.4 the calculation stops without an error message. The
curios thing is, that the programs runs without any
problems at other lambda steps 0.2, 0.5, 0.6, 0.7, 0.8 and 0.9.
I use amber 11 with bug-fix 0_1
Could anyone help me indicate why this happens?
Thank you.
Kirsten Heitmann
*********************************************
The outputfile looks like this:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 09/19/2010 at 21:54:35
[-O]verwriting output
...
Here is the input file:
density
minlibration
&cntrl
imin = 1, ntx =
1,
maxcyc =
500,
ntpr =
100,
ntf = 2, ntc =
1,
ntb = 1, cut =
12.0,
icfe = 1, clambda =
0.1,
ifsc=0,
crgmask=':1,10,11,20',
&end
....
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 6742675
| TOTAL SIZE OF NONBOND LIST = 6742675
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Received on Thu Sep 30 2010 - 00:30:03 PDT
