Error running deinterleave_idws.py on FEP simulation output

From: Amy Rice (arice3_at_hawk.iit.edu)
Date: Wed Feb 13 2019 - 12:42:10 CST

Hi all,
I am testing a FEP simulation using NAMD 2.13 with IDWS. To test my system,
I ran a very short FEP simulation with only 100 steps per lambda value,
with lambda from 0 to 1 in increments of 0.1. The simulation completed
without error, but I am unable to postprocess the fep output with
deinterleave_idws.py. When I run the python script, I get the following
error:

Traceback (most recent call last):
  File "./deinterleave_idws.py", line 199, in <module>
    wb.steps.append(step_counter)
NameError: name 'wb' is not defined

>From what I can tell, the problem is that my FEP output file does not match
the format expected by the python script- my output file has 10 columns but
the script seems to expect 11 if IDWS is on (line 291):

        if len(fields) == 11:
            cur_lambdaIDWS = float(fields[10])
            IDWS_on = True
            wb = Window(cur_lambda1, cur_lambdaIDWS)

It also seems that the script expects a line in the FEP out file that
starts with "#NEW FEP WINDOW:" each time lambda is changed, but this is not
the case in my FEP out file (line 206 of deinterleave_idws.py):

    elif line.startswith('#NEW FEP WINDOW:'):

        if step_counter >= 0:
            first_window = False
        step_counter = -1

        # Extract lambda values
        cur_lambda1 = float(fields[6])
        cur_lambda2 = float(fields[8])

A sample of the FEP output has been pasted below, and the full file
(test.fep) can be found here:
http://s000.tinyupload.com/index.php?file_id=95505654457461737276

 The relevant portion of my configuration file is also given below.

Any insight into why the FEP output file format is not as expected? Is it
possible I'm missing a required option in the configuration file?

Thank you for the help,
Amy

---------------------------- test.fep ---------------------------

# STEP Elec
vdW dE dE_avg Temp dG
# l l+dl l
l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.1
FepEnergy: 5 -81561.5747 -81506.2895 7468.1313
7461.7973 48.9512 48.6513 308.8818 48.5899
FepEnergy: 10 -81593.6226 -81538.5728 7497.7188
7490.0548 47.3857 48.4042 308.3850 48.1867
FepEnergy: 15 -81745.3745 -81689.8651 7623.0471
7615.3590 47.8213 48.1149 308.6998 47.8489
FepEnergy: 20 -81851.9507 -81796.4133 7658.7396
7651.0947 47.8925 48.0701 310.0615 47.8659
FepEnergy: 25 -81693.8541 -81639.4306 7530.8473
7524.5452 48.1213 48.1016 309.4985 47.9205
FepEnergy: 30 -81632.5928 -81579.6824 7518.5800
7512.0492 46.3795 47.9520 307.9105 47.6241
FepEnergy: 35 -81644.3630 -81591.4959 7466.7152
7459.4200 45.5719 47.6439 308.6566 46.7768
FepEnergy: 40 -81645.4509 -81591.0092 7500.0850
7491.1633 45.5200 47.3799 308.2222 46.3875
FepEnergy: 45 -81758.6129 -81703.4411 7571.9448
7562.5530 45.7800 47.2073 309.9286 46.2855
#50 STEPS OF EQUILIBRATION AT LAMBDA 0 COMPLETED
#STARTING COLLECTION OF ENSEMBLE AVERAGE
FepEnergy: 50 -81581.0032 -81526.4651 7515.4610
7505.1362 44.2134 44.2134 306.9747 44.2134
FepEnergy: 55 -81362.4304 -81309.3919 7323.1291
7314.7191 44.6284 44.3384 306.7312 44.3105
FepEnergy: 60 -81368.2063 -81315.4191 7263.0966
7256.0697 45.7603 44.6604 309.1481 44.5204
FepEnergy: 65 -81352.0983 -81298.6321 7272.1913
7266.3589 47.6338 45.4301 307.3889 44.7456
FepEnergy: 70 -81638.5477 -81586.7070 7506.9008
7502.1082 47.0481 45.8778 308.2766 44.9100
FepEnergy: 75 -81888.1600 -81834.6793 7677.8265
7672.0645 47.7186 46.1616 310.2054 45.0385
FepEnergy: 80 -81875.4077 -81820.1817 7660.5578
7653.5767 48.2449 46.4679 310.2780 45.1460
FepEnergy: 85 -81831.9312 -81776.4447 7626.5606
7619.8681 48.7940 46.7720 309.8195 45.2378
FepEnergy: 90 -81780.4173 -81725.4238 7574.9458
7567.8352 47.8828 46.9599 310.5496 45.3172
FepEnergy: 95 -81766.2386 -81712.4073 7502.8241
7495.2230 46.2302 46.9459 311.3023 45.3798
FepEnergy: 100 -81581.0306 -81527.8560 7436.1630
7429.6158 46.6274 46.8792 308.3985 45.4268
#Free energy change for lambda window [ 0 0.1 ] is 45.4268 ; net change
until now is 45.4268
FepEnergy: 105 -81391.5170 -81339.6430 7400.1083
7396.9320 48.6977 48.6977 307.1903 48.6977
FepE_back: 110 -81379.0425 -81428.8655 7401.1905
7408.9307 -42.0828 47.4868 307.2172 47.1151
FepEnergy: 115 -81501.3646 -81449.2581 7380.9194
7377.0670 48.2541 47.6147 310.8916 47.2083
FepE_back: 120 -81564.0116 -81618.3442 7393.9807
7404.2930 -44.0203 48.2551 311.5470 47.5046
FepEnergy: 125 -81501.1474 -81447.6114 7452.7233
7446.6003 47.4131 48.1786 308.7367 47.4957
FepE_back: 130 -81616.1229 -81669.9141 7547.6673
7560.7802 -40.6783 47.8927 309.9197 47.3605
FepEnergy: 135 -81701.9051 -81647.3888 7563.1911
7555.8314 47.1566 47.8467 311.2957 47.3456
FepE_back: 140 -81719.7588 -81771.8062 7561.2876
7578.0790 -35.2560 47.4253 311.1195 46.2893
FepEnergy: 145 -81621.2661 -81569.9290 7538.8871
7528.8656 41.3156 47.1343 308.4667 43.1873
#50 STEPS OF EQUILIBRATION AT LAMBDA 0.1 COMPLETED
#STARTING COLLECTION OF ENSEMBLE AVERAGE
FepE_back: 150 -81539.3137 -81591.3598 7437.7531
7456.3702 -33.4289 -nan 307.8654 nan
FepEnergy: 155 -81387.0328 -81334.3667 7317.0034
7308.2923 43.9551 43.9551 306.3730 43.9551

--------------------------- FEP.conf --------------------------
#alchemical
alch on
alchType fep
alchFile tLPS_121A.fep
alchCol B
alchOutFreq 5
alchEquilSteps 50

alchLambda 0.0
alchLambda2 0.1
run 100

set Lambda0 0.1
set dLambda 0.1

while {$Lambda0 < 0.9} {
 alchLambda $Lambda0
 set LambdaB [expr $Lambda0 - $dLambda]
 set Lambda0 [expr $Lambda0 + $dLambda]
 alchLambda2 $Lambda0
 alchLambdaIDWS $LambdaB
 run 100
}
-----------------------------------------------------------------

PS- I apologize if this message appears twice in the mailing list. I sent
it earlier today but never saw it sent out so I am trying again without any
file attachments.

-- 
Amy Rice
Ph.D. Candidate
Physics Department
Illinois Institute of Technology

This archive was generated by hypermail 2.1.6 : Thu Dec 12 2019 - 23:20:27 CST