From: Maryam Sayadi (maryam.sayadi_at_gmail.com)
Date: Sun Feb 16 2014 - 14:04:12 CST
Dear all,
I have some questions about TI calculations in NAMD.
>First, I get the error message "Warning: one or more integrands were
worryingly large (>30)" with the output of :
|------------------------------------------------------------ |
| | elec | vdW | Subtotal |
|------------------------------------------------------------ |
| Part. 1 | 0.0553 | 2.2673 | 2.3225 |
| Part. 2 | -441.3303 | 221.5677 | -219.7625 |
|---------------------------------------------------------------|
| Subtotal | 441.3855 | -219.3005 | 222.0851 |
|---------------------------------------------------------------|
Does any body know if it is common to have large integrands only in one
part and not in both?
>Second, Here is the detailed dE/Dl values for part 2 :
Partition 2 electrostatics
Lambda dE/dl Area Total
0.0000000 -6.785823 -60.329838 -60.329838
0.1111110 -997.166076 -115.778322 -176.108160
0.2222220 -1003.711135 -112.844237 -288.952396
0.3333330 -996.475380 -92.645559 -381.597955
0.4444440 -630.879148 -41.623990 -423.221946
0.5555560 -140.433098 -7.770879 -430.992825
0.6666670 -39.872596 -3.694406 -434.687231
0.7777780 -34.585969 -3.553706 -438.240937
0.8888890 -29.535681 -2.796706 -441.037643
0.9888890 -26.531512 -0.262867 -441.300510
0.9988890 -26.217190 -0.026723 -441.327234
0.9998890 -27.356136 -0.003028 -441.330261
1.0000000 -27.144267 N/A -441.330261
Partition 2 vdW
Lambda dE/dl Area Total
0.0000000 -3.441897 -0.003380 -0.003380
0.0010000 -3.328854 -0.028273 -0.031652
0.0100000 -3.007128 -0.527328 -0.558980
0.1000000 -2.532830 3.185349 2.626368
0.2000000 76.780826 13.143806 15.770174
0.3000000 207.946794 37.587088 53.357262
0.4000000 549.478545 67.278414 120.635676
0.5000000 748.847397 66.469328 187.105004
0.6000000 523.471178 27.157656 214.262659
0.7000000 38.024283 1.541237 215.803896
0.8000000 32.756213 2.942152 218.746049
0.9000000 26.778381 2.523643 221.269691
0.9900000 29.956264 0.267894 221.537585
0.9990000 29.633870 0.027120 221.564705
0.9999000 30.625582 0.003022 221.567727
1.0000000 29.658783 N/A 221.567727
I tried finer sampling in the regions where dE/dl is large ( 0.3
<Lambda<0.6) to get a smoother curve . Still got the same curve. Does any
body have any suggestions ?
>Third, I noticed that during the simulation, my helical structure unfolds!
Have anybody any experience with unstable systems in TI ?
Regards,
Maryam
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