Mercurial > repos > chemteam > biomd_rmsd_clustering
changeset 1:b001ebc8bf58 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
| author | chemteam |
|---|---|
| date | Fri, 11 Sep 2020 21:55:34 +0000 |
| parents | ee1f38eb220e |
| children | b9c46dbe9605 |
| files | NEQGamma.py test-data/NEQGamma_clusters.json test-data/NEQGamma_ofrict.txt test-data/NEQGamma_ofrict1.txt test-data/NEQGamma_ofrict2.txt test-data/NEQGamma_outp.txt test-data/NEQGamma_outp1.txt test-data/NEQGamma_outp2.txt test-data/pull1.xvg test-data/pull2.xvg test-data/pull3.xvg |
| diffstat | 11 files changed, 1177 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NEQGamma.py Fri Sep 11 21:55:34 2020 +0000 @@ -0,0 +1,210 @@ +#!/usr/bin/env python + +# coding: utf-8 +# This script is a modified version of a script written +# by Steffen Wolf under the GPL v3.0. +# The original version can be accessed at +# https://github.com/moldyn/dcTMD/blob/master/NEQGamma.py + +import argparse +import json +import sys + +import numpy as np + +import pandas as pd + +import scipy +import scipy.integrate +from scipy.ndimage.filters import gaussian_filter + + +def get_file_names(list_file): + with open(list_file) as f: + return [line for line in f.read().split('\n') if line] + + +def NEQGamma(file_names, output, output_frict, vel, T, av, sigma): + N = len(file_names) + RT = 0.0083144598 * T + + sys.stdout.write("reading data...\n") + + # read in initial data to get length of necessary array + test_file = pd.read_csv(file_names[0], delim_whitespace=True, + header=None, skiprows=17, dtype=float) + length_data = len(test_file[0].values) + full_force_set = np.zeros((N, length_data)) + x = np.zeros(length_data) + t = np.zeros(length_data) + t = test_file[0].values + x = test_file[0].values * vel + + # read in data + for i in range(0, N): + current_file_name = file_names[i] + sys.stdout.write("reading file {}\n".format(current_file_name)) + input_file_data = pd.read_csv(current_file_name, delim_whitespace=True, + header=None, skiprows=17, dtype=float) + full_force_set[i, :] = input_file_data[1].values + + # preprocessing + # * force average: calculate $\left< f_c (t)\right>_N$. + # **Important:** this is an ensemble average over the trajectory ensemble + # $N$, not the time average over $t$ + av_force = np.zeros(length_data) + av_forceintegral = np.zeros(length_data) + for i in range(length_data): + av_force[i] = np.mean(full_force_set[:, i]) + av_forceintegral[1:] = scipy.integrate.cumtrapz(av_force, x) + + # calculate $\delta f_c(t) = f_c(t) - \left< f_c (t) \right>_N$ for all $t$ + sys.stdout.write("calculating fluctuations...\n") + delta_force_set = np.zeros((N, length_data)) + for i in range(length_data): + delta_force_set[:, i] = full_force_set[:, i] - av_force[i] + + # evaluation + # * optimized algorithm for numerical evaluation: + # * integrate: $\int_0^t dt' \delta f_c(t')$ for all $t'$ + # * multiply by $\delta f_c(t)$ to yield + # $\int_0^t dt'\delta f_c(t) \delta f_c(t')$ for $t$ + # with all $t' \leq t$ each + # * then calculate the ensemble average + # $\left< \int_0^t dt' \delta f_c(t) \delta f_c(t') \right>$ + int_delta_force_set = np.zeros((N, length_data)) + for n in range(N): + int_delta_force_set[n, 1:] = scipy.integrate.cumtrapz( + delta_force_set[n, :], t) + + sys.stdout.write("averaging and integrating...\n") + intcorr = np.zeros((N, length_data)) + + for n in range(N): + for i in range(length_data): + intcorr[n, i] = delta_force_set[n, i] * int_delta_force_set[n, i] + if i % 1000 == 0: + sys.stdout.write("Trajectory {:2d} {:3.1f} % done\r".format( + n + 1, (i / length_data) * 100)) + + # shape of $\int_0^t dt' \delta f_c(t) \delta f_c(t')$: + sys.stdout.write("final average...\n") + av_intcorr = np.zeros(length_data) + for i in range(length_data): + av_intcorr[i] = np.mean(intcorr[:, i]) / RT + + # autocorrelation function evaluation: + # * calculate $\left< \delta f_c(t) \delta f_c(t') \right>$ + # for the last $t$ + + corr_set = np.zeros((N, length_data)) + autocorr_set = np.zeros(length_data) + + sys.stdout.write("calculating and processing ACF...\n") + for n in range(N): + for i in range(length_data): + corr_set[n, i] = delta_force_set[ + n, i] * delta_force_set[n, length_data - 1] + + for i in range(length_data): + autocorr_set[i] = np.mean(corr_set[:, i]) + + # * Gauss filter: + sys.stdout.write("applying Gauss filter...\n") + blurr = sigma + blurred = np.zeros(length_data) + blurred = gaussian_filter(av_intcorr, sigma=blurr) + + # * sliding window average: + sys.stdout.write("applying sliding window average...\n") + window = av + runn_av = np.zeros(length_data) + runn_av = np.convolve(av_intcorr, np.ones((window,)) / window, mode='same') + + # * $W_{diss}$ from integration: + wdiss = np.zeros(length_data) + wdiss[1:] = scipy.integrate.cumtrapz(av_intcorr, x) * vel + + sys.stdout.write("writing output...\n") + dist = open(output, "w") + frict = open(output_frict, "w") + + dist.write( + "#x force_integral frict_coeff wdiss corrected_force_integral\n") + for i in range(length_data): + dist.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format( + x[i], av_forceintegral[i], av_intcorr[i], wdiss[i], + av_forceintegral[i] - wdiss[i])) + + frict.write("""#x ACF frict_coeff """ + """gauss_filtered_frict_coeff av_window_frict_coeff\n""") + for i in range(length_data): + frict.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format( + x[i], autocorr_set[i], av_intcorr[i], blurred[i], runn_av[i])) + + dist.close() + frict.close() + + sys.stdout.write("Done!\n") + + +def main(): + parser = argparse.ArgumentParser(description="""dcTMD friciton correction + (please cite: Wolf, S., Stock, G. Targeted Molecular Dynamics + Calculations of Free Energy Profiles Using a Nonequilibrium + Friction Correction. J. Chem. Theory Comput. 2018, 14(12), 6175-6182, + DOI: 10.1021/acs.jctc.8b00835). Integrates a constraint force file via + trapezoid rule, calculates the NEQ memory friction kernel and friction + factors, and performs a friction correction. First column: reaction + coordinate in nm calculated via t * vel. Second column: force integral, + i.e. the work profile. Third column: friction factors. Fourth column: + trapezoid integral (final value) of friction work along reaction + coordinate. Fourth column: friction corrected work profile. ATTENTION: + Use with python3 or higher!""") + parser.add_argument('-i', metavar='<xvg force file>', type=str, + help="""List of xvg constraint force files prefix + as given by Gromacs mdrun -pf option before running + number.""") + parser.add_argument('-o', metavar='<combined results>', type=str, + help="""file to write x, dG(x), friction coefficeint by + integration (time resolved), and the friction-corrected + dG(x).""") + parser.add_argument('-ofrict', metavar='<combined friction results>', + type=str, + help="""file to write x, ACF, friction coefficeint by + integration (time resolved), gauss filtered friction + coefficient, and slide window averaged friction.""") + parser.add_argument('-vel', metavar='<pull velocity>', type=float, + help="""pull velocity in nm/ps for converting simulation + time t into distance x""") + parser.add_argument('-T', metavar='<temperature>', type=float, + help='temperature in K') + parser.add_argument('-av', metavar='<average window>', type=int, + help="""size of averaging window for displaying + Gamma(x) (recommended: 4 to 20 per 100 data points)""") + parser.add_argument('-sigma', metavar='<gauss blurr>', type=int, + help="""sigma value for Gauss filter for displaying + Gamma(x) (recommended: 4 per 100 data points)""") + parser.add_argument('-json', metavar='<json>', type=str, + help='JSON file defining cluster membership') + + args = parser.parse_args() + + file_names = get_file_names(args.i) + if args.json: + with open(args.json) as f: + j = json.load(f) + file_names_dct = {n: [file_names[int(m)] for m in j[n]] for n in j} + + for cluster in file_names_dct: + NEQGamma(file_names_dct[cluster], + 'cluster{}_{}'.format(cluster, args.o), + 'cluster{}_{}'.format(cluster, args.ofrict), + args.vel, args.T, args.av, args.sigma) + else: + NEQGamma(file_names, args.o, args.ofrict, args.vel, + args.T, args.av, args.sigma) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_clusters.json Fri Sep 11 21:55:34 2020 +0000 @@ -0,0 +1,1 @@ +{"0": ["0", "1"], "1": ["0", "2"]}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_ofrict.txt Fri Sep 11 21:55:34 2020 +0000 @@ -0,0 +1,102 @@ +#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff + 0.00000000 439653.22756622 0.00000000 39.85704130 -164.30975524 + 0.00000200 41861.51118060 -309.80490686 39.90128147 -42.50284457 + 0.00000400 -4760.58383990 -1433.31122481 39.98937507 132.75776205 + 0.00000600 -52063.97568219 -1302.42266399 40.10796653 273.24484877 + 0.00000800 -94137.43307581 -696.00283593 40.26787861 322.90057440 + 0.00001000 -109240.44374298 59.67135417 40.47438205 310.49706801 + 0.00001200 -91296.29474097 200.26534006 40.74119359 300.71687201 + 0.00001400 -42279.73264591 -211.00314767 41.08344474 307.77939795 + 0.00001600 29083.13222726 -299.86397145 41.51045417 289.59363364 + 0.00001800 100957.95082594 706.27695160 42.02391473 213.62523715 + 0.00002000 150492.32652407 2436.13821354 42.62185633 115.80351000 + 0.00002200 163610.52308989 3505.21213240 43.30185229 72.52474633 + 0.00002400 137798.21546909 2809.74173435 44.06395945 119.32042200 + 0.00002600 86552.97296922 993.11451262 44.91354630 219.23877027 + 0.00002800 30065.89230936 -248.07012791 45.85833909 214.16642537 + 0.00003000 -15271.83960767 -195.60392001 46.90428227 107.42336841 + 0.00003200 -41143.37576909 141.25051892 48.05595140 -10.23715919 + 0.00003400 -45603.75654834 -363.71528632 49.31891708 -41.13071129 + 0.00003600 -31933.14574422 -1519.36792976 50.67717643 11.13789839 + 0.00003800 -11580.24564270 -1956.43454302 52.14035913 47.86749694 + 0.00004000 1795.96943076 -865.57527338 53.69638462 -13.42971260 + 0.00004200 -6069.40567724 626.10860652 55.34660090 -151.70147237 + 0.00004400 -36605.44103603 565.05574074 57.08967355 -284.06117371 + 0.00004600 -88409.03954732 -1403.86956218 58.91185508 -352.46208669 + 0.00004800 -119187.64656330 -2830.86397506 60.79652934 -358.13736161 + 0.00005000 -126958.63383213 -2293.53919791 62.72537859 -329.02117947 + 0.00005200 -105144.23378691 -417.60570188 64.67974189 -286.64057459 + 0.00005400 -57578.18477311 834.36904591 66.64059843 -231.16675138 + 0.00005600 7642.76668942 434.72799961 68.58976595 -160.41908396 + 0.00005800 73314.58537446 -519.66723923 70.51136345 -97.11322986 + 0.00006000 117239.42596973 -329.29698187 72.38916035 -71.95507125 + 0.00006200 122335.84589389 858.01810556 74.20116994 -72.69735215 + 0.00006400 90700.59252948 1441.72347492 75.92201577 -50.06936146 + 0.00006600 40928.26316446 879.60901414 77.52654008 55.63484244 + 0.00006800 -3181.66487546 334.25351485 78.99192675 197.17614864 + 0.00007000 -31227.72623817 652.00817770 80.29696328 378.84255238 + 0.00007200 -43642.08135556 1250.72698300 81.42019653 507.21229626 + 0.00007400 -37578.91493866 1051.23806218 82.34208812 533.01944777 + 0.00007600 -9313.59450148 -253.25084775 83.04041098 497.57963010 + 0.00007800 35606.42432047 -1453.27137086 83.53076487 484.49556872 + 0.00008000 74825.06321773 -880.42089139 83.79365831 512.38603041 + 0.00008200 87450.95751560 1078.66842032 83.81028733 508.57269634 + 0.00008400 84964.54130532 2679.13981866 83.55962529 417.18682766 + 0.00008600 33723.38650302 1426.95656188 83.03964822 275.01069883 + 0.00008800 26888.00526112 802.46409967 82.26457780 159.07974622 + 0.00009000 15764.22367820 273.85567979 81.25039304 86.68872404 + 0.00009200 -1018.04050367 98.53732822 80.00383608 19.95207715 + 0.00009400 -18778.21955924 125.57269254 78.52437737 -55.26075096 + 0.00009600 -25696.85381088 173.04677203 76.81790266 -95.82294253 + 0.00009800 -19020.27963144 38.14199457 74.90534804 -40.08283716 + 0.00010000 -13853.36236626 -405.56366316 72.81359766 112.25327202 + 0.00010200 -22360.23253615 -969.69926808 70.56500733 263.50051564 + 0.00010400 -39525.81005506 -1401.79910164 68.18385377 320.37515633 + 0.00010600 -47887.23125912 -1439.01003806 65.70767268 323.43291333 + 0.00010800 -38703.50620624 -1113.56692890 63.18337712 284.23466280 + 0.00011000 -15756.47051989 -682.72476001 60.65377002 277.77044438 + 0.00011200 10148.75573217 -253.52957929 58.15278984 250.27515323 + 0.00011400 32489.76783313 239.99423089 55.71193773 178.79248872 + 0.00011600 48846.14416151 861.55125965 53.36798832 70.38368037 + 0.00011800 60211.15804332 1593.45081266 51.19169051 -55.24610237 + 0.00012000 64597.66151097 2144.52398093 49.22113114 -170.30467384 + 0.00012200 58795.32774769 2216.16123424 47.49918918 -248.93156307 + 0.00012400 63226.50291119 2740.29495857 46.05677747 -270.24081648 + 0.00012600 7112.67333129 642.99155129 44.93086250 -206.96775261 + 0.00012800 4737.67676382 673.17973142 44.16608448 -50.37244372 + 0.00013000 -10629.83066809 -276.05014319 43.80477020 154.04681427 + 0.00013200 -24445.08596782 -1331.11596207 43.87860095 320.32723893 + 0.00013400 -38089.44576760 -2042.60347448 44.40990189 378.66585808 + 0.00013600 -53888.48385453 -2339.54888278 45.42258092 320.31441637 + 0.00013800 -65525.93331796 -2263.02943488 46.94717499 192.76961767 + 0.00014000 -66605.80950981 -1978.10144773 49.01173919 46.49351043 + 0.00014200 -59461.87405093 -1395.88433631 51.62964197 -100.43225450 + 0.00014400 -50082.83777468 -136.33782409 54.79891493 -258.31822307 + 0.00014600 -36265.73051644 1692.89613965 58.50910094 -447.27992440 + 0.00014800 -11065.11218743 2974.81823090 62.74931610 -601.98154580 + 0.00015000 24574.77396976 2642.88373319 67.50830566 -716.60080679 + 0.00015200 53704.30727291 913.24280375 72.76914377 -754.65637852 + 0.00015400 62641.21173742 -927.03460327 78.50486320 -713.36174226 + 0.00015600 50475.22167026 -1689.34471443 84.67941051 -602.77004154 + 0.00015800 27415.48879178 -1332.07133205 91.25069147 -429.82867913 + 0.00016000 659.52027909 -793.99131765 98.16114225 -214.90982911 + 0.00016200 -27358.17056213 -941.55813718 105.35683648 -1.93703392 + 0.00016400 -36359.81639946 -1038.93906805 112.78930315 141.63166343 + 0.00016600 -103478.83628142 -2451.04087672 120.41222030 155.07119820 + 0.00016800 -98122.08801466 -1619.20548854 128.15466148 39.58301004 + 0.00017000 -91470.31369949 -1037.16157762 135.94071127 -128.72347744 + 0.00017200 -70167.76251890 -505.22323695 143.69516807 -240.17685720 + 0.00017400 -43298.45234300 169.23053990 151.35171103 -223.11938998 + 0.00017600 -13147.13005351 1119.27836540 158.84649112 -87.45006406 + 0.00017800 13812.88135432 2035.34756564 166.10612536 85.27603300 + 0.00018000 29405.90836664 2281.35445610 173.04701036 209.91332866 + 0.00018200 27785.78282904 1475.48961051 179.59291666 253.65425754 + 0.00018400 16400.24253711 132.45287134 185.68841711 300.73216440 + 0.00018600 5032.51740518 -616.86762340 191.28914198 352.67911780 + 0.00018800 -684.42414340 -391.31151887 196.34017758 475.23116164 + 0.00019000 -2606.74806622 413.81613798 200.77390679 556.19143606 + 0.00019200 -4228.75142469 1254.39214820 204.53041970 608.04951495 + 0.00019400 -2944.53596867 1786.35191510 207.57544804 633.31067679 + 0.00019600 4064.05842526 1765.17722675 209.89395091 624.84914980 + 0.00019800 11878.81314410 1160.67458116 211.46967661 568.88523153 + 0.00020000 12188.47862387 80.82726004 212.27097983 467.11785325
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NEQGamma_ofrict1.txt Fri Sep 11 21:55:34 2020 +0000 @@ -0,0 +1,102 @@ +#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff + 0.00000000 -131993.41016925 0.00000000 -31.41159270 -71.62375840 + 0.00000200 16345.04469682 -1345.26646099 -31.23092179 16.85099383 + 0.00000400 29113.39120702 -1454.28761686 -30.88206666 43.12225366 + 0.00000600 27656.43517472 -264.14035591 -30.38447804 -24.61744170 + 0.00000800 22081.05883970 570.71230720 -29.75116213 -124.82229209 + 0.00001000 9926.50084650 482.67878751 -28.98362546 -148.88674802 + 0.00001200 -5957.22964270 -306.50010800 -28.07154561 -44.25804572 + 0.00001400 -21071.08253355 -678.79838871 -27.00311927 120.09671342 + 0.00001600 -30206.93805045 129.24578885 -25.77749754 210.63856614 + 0.00001800 -30292.41328536 1433.88087902 -24.40797512 147.07777675 + 0.00002000 -21089.95150080 1769.49504443 -22.91494801 -14.98005248 + 0.00002200 -5123.22129025 525.42519661 -21.31752461 -139.14697408 + 0.00002400 14086.19434495 -1354.79390711 -19.63003766 -71.97480155 + 0.00002600 31413.15161600 -2004.09700782 -17.86212814 78.50640859 + 0.00002800 42209.76106550 -481.28911857 -16.02210724 139.74809987 + 0.00003000 42689.48379010 2092.57404588 -14.11799868 71.98635054 + 0.00003200 32140.35686690 3287.09518295 -12.15586303 -24.51897016 + 0.00003400 13442.16919797 1810.83705441 -10.14236807 -39.10004376 + 0.00003600 -9231.10226605 -1271.21578790 -8.09221902 20.27669074 + 0.00003800 -29408.62646120 -3241.15658461 -6.02052658 45.55495337 + 0.00004000 -41627.31520850 -2483.33843193 -3.94447769 -27.79664184 + 0.00004200 -42137.13334250 -1.82301038 -1.86595819 -140.52649008 + 0.00004400 -30226.42411600 1555.33658588 0.21546106 -185.57828610 + 0.00004600 -11806.47895017 960.69346965 2.28847531 -122.35443556 + 0.00004800 9446.43397092 -784.52267942 4.34049778 -10.01090329 + 0.00005000 24611.29240972 -1447.42762641 6.35945779 66.73347194 + 0.00005200 30168.44061035 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pull1.xvg Fri Sep 11 21:55:34 2020 +0000 @@ -0,0 +1,118 @@ +# This file was created Sat Jan 11 15:16:55 2020 +# Created by: +# :-) GROMACS - gmx mdrun, 2019.1 (-: +# +# Executable: /usr/local/bin/gmx +# Data prefix: /usr/local +# Working dir: /data/share/staging/6673623/working +# Command line: +# gmx mdrun -nt 16 -deffnm outp +# gmx mdrun is part of G R O M A C S: +# +# God Rules Over Mankind, Animals, Cosmos and Such +# +@ title "Pull force" +@ xaxis label "Time (ps)" +@ yaxis label "Force (kJ/mol/nm)" +@TYPE xy +0.0000 6024.09 +0.0020 -1440.45 +0.0040 -2511.27 +0.0060 -2897.63 +0.0080 -2775.86 +0.0100 -1984.12 +0.0120 -692.582 +0.0140 749.852 +0.0160 1926.04 +0.0180 2521.88 +0.0200 2405.94 +0.0220 1618.47 +0.0240 312.892 +0.0260 -1146.03 +0.0280 -2331.23 +0.0300 -2868.38 +0.0320 -2634.84 +0.0340 -1742.36 +0.0360 -463.328 +0.0380 764.038 +0.0400 1581.21 +0.0420 1724.85 +0.0440 1203.93 +0.0460 119.215 +0.0480 -933.681 +0.0500 -1649.19 +0.0520 -1728.6 +0.0540 -1128.9 +0.0560 -43.2839 +0.0580 1061.76 +0.0600 1706.84 +0.0620 1632.03 +0.0640 886.953 +0.0660 -265.667 +0.0680 -1413.95 +0.0700 -2156.87 +0.0720 -2271.91 +0.0740 -1707.92 +0.0760 -561.06 +0.0780 847.304 +0.0800 1993.62 +0.0820 2439.33 +0.0840 2183.08 +0.0860 1162.58 +0.0880 245.372 +0.0900 -674.664 +0.0920 -1389.64 +0.0940 -1732.39 +0.0960 -1659.95 +0.0980 -1215.14 +0.1000 -560.687 +0.1020 56.7457 +0.1040 541.266 +0.1060 941.849 +0.1080 1290.27 +0.1100 1550.28 +0.1120 1620.82 +0.1140 1483.18 +0.1160 1200.91 +0.1180 835.327 +0.1200 414.748 +0.1220 -21.986 +0.1240 -268.239 +0.1260 -610.519 +0.1280 -419.701 +0.1300 -193.452 +0.1320 11.4089 +0.1340 13.1112 +0.1360 -276.636 +0.1380 -829.048 +0.1400 -1451.56 +0.1420 -1907.91 +0.1440 -1960.87 +0.1460 -1495.45 +0.1480 -590.751 +0.1500 498.442 +0.1520 1444.86 +0.1540 2030.3 +0.1560 2092.26 +0.1580 1656.44 +0.1600 859.3 +0.1620 14.6479 +0.1640 -438.284 +0.1660 -573.584 +0.1680 32.1338 +0.1700 805.322 +0.1720 1470.23 +0.1740 1733.74 +0.1760 1558.83 +0.1780 971.192 +0.1800 103.252 +0.1820 -825.594 +0.1840 -1427.63 +0.1860 -1342.79 +0.1880 -578.404 +0.1900 513.202 +0.1920 1414.83 +0.1940 1795.16 +0.1960 1584.51 +0.1980 877.231 +0.2000 -111.269
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pull2.xvg Fri Sep 11 21:55:34 2020 +0000 @@ -0,0 +1,118 @@ +# This file was created Sat Jan 11 15:14:02 2020 +# Created by: +# :-) GROMACS - gmx mdrun, 2019.1 (-: +# +# Executable: /usr/local/bin/gmx +# Data prefix: /usr/local +# Working dir: /data/share/staging/6673627/working +# Command line: +# gmx mdrun -nt 16 -deffnm outp +# gmx mdrun is part of G R O M A C S: +# +# GROup of MAchos and Cynical Suckers +# +@ title "Pull force" +@ xaxis label "Time (ps)" +@ yaxis label "Force (kJ/mol/nm)" +@TYPE xy +0.0000 -5098.38 +0.0020 -63.1292 +0.0040 -58.0201 +0.0060 -567.151 +0.0080 -915.192 +0.0100 -1147.66 +0.0120 -1194.57 +0.0140 -1025.71 +0.0160 -619.358 +0.0180 -30.7206 +0.0200 628.788 +0.0220 1186.76 +0.0240 1499.87 +0.0260 1501.01 +0.0280 1225.59 +0.0300 728.864 +0.0320 73.4782 +0.0340 -609.651 +0.0360 -1241.19 +0.0380 -1714.09 +0.0400 -1926.53 +0.0420 -1825.85 +0.0440 -1343.11 +0.0460 -875.662 +0.0480 -137.674 +0.0500 424.689 +0.0520 813.554 +0.0540 1028.83 +0.0560 1080.86 +0.0580 1012.46 +0.0600 876.583 +0.0620 713.725 +0.0640 570.333 +0.0660 475.042 +0.0680 392.949 +0.0700 224.142 +0.0720 -50.0798 +0.0740 -394.081 +0.0760 -697.375 +0.0780 -847.788 +0.0800 -757.177 +0.0820 -440.838 +0.0840 160.155 +0.0860 304.292 +0.0880 804.365 +0.0900 951.843 +0.0920 801.215 +0.0940 418.322 +0.0960 -64.6304 +0.0980 -449.703 +0.1000 -559.593 +0.1020 -338.869 +0.1040 98.9362 +0.1060 546.434 +0.1080 882.254 +0.1100 1007.2 +0.1120 882.558 +0.1140 546.07 +0.1160 148.665 +0.1180 -57.5016 +0.1200 49.9737 +0.1220 409.28 +0.1240 1040.8 +0.1260 684.824 +0.1280 692.54 +0.1300 134.317 +0.1320 -629.767 +0.1340 -1376.01 +0.1360 -1941.02 +0.1380 -2059.37 +0.1400 -1616.22 +0.1420 -670.138 +0.1440 475.235 +0.1460 1491.31 +0.1480 2085.01 +0.1500 2105.1 +0.1520 1531.93 +0.1540 553.708 +0.1560 -497.426 +0.1580 -1283.86 +0.1600 -1568.59 +0.1620 -1327.71 +0.1640 -455.275 +0.1660 -393.621 +0.1680 265.539 +0.1700 336.479 +0.1720 66.7614 +0.1740 -435.565 +0.1760 -1029.08 +0.1780 -1534.97 +0.1800 -1795.16 +0.1820 -1760.74 +0.1840 -1399.95 +0.1860 -849.902 +0.1880 -285.645 +0.1900 176.529 +0.1920 484.836 +0.1940 615.295 +0.1960 570.901 +0.1980 319.342 +0.2000 -63.7999
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pull3.xvg Fri Sep 11 21:55:34 2020 +0000 @@ -0,0 +1,118 @@ +# This file was created Sat Jan 11 11:17:19 2020 +# Created by: +# :-) GROMACS - gmx mdrun, 2019.1 (-: +# +# Executable: /usr/local/bin/gmx +# Data prefix: /usr/local +# Working dir: /data/share/staging/6671882/working +# Command line: +# gmx mdrun -nt 16 -deffnm outp +# gmx mdrun is part of G R O M A C S: +# +# Gyas ROwers Mature At Cryogenic Speed +# +@ title "Pull force" +@ xaxis label "Time (ps)" +@ yaxis label "Force (kJ/mol/nm)" +@TYPE xy +0.0000 -9835.61 +0.0020 -1356.15 +0.0040 -812.913 +0.0060 -356.365 +0.0080 279.129 +0.0100 695.388 +0.0120 760.799 +0.0140 413.1 +0.0160 -307.339 +0.0180 -1119.04 +0.0200 -1694.31 +0.0220 -1857.34 +0.0240 -1599.83 +0.0260 -1103.08 +0.0280 -590.412 +0.0300 -216.222 +0.0320 -59.4561 +0.0340 -111.021 +0.0360 -349.112 +0.0380 -631.665 +0.0400 -749.358 +0.0420 -480.318 +0.0440 251.563 +0.0460 1193.69 +0.0480 1913.5 +0.0500 2185.92 +0.0520 1987.19 +0.0540 1406.94 +0.0560 543.203 +0.0580 -401.431 +0.0600 -1124.73 +0.0620 -1356.63 +0.0640 -1090.51 +0.0660 -579.76 +0.0680 -169.391 +0.0700 10.7899 +0.0720 33.8781 +0.0740 -114.673 +0.0760 -468.487 +0.0780 -956.942 +0.0800 -1266.95 +0.0820 -1152.33 +0.0840 -799.059 +0.0860 -57.2971 +0.0880 86.3943 +0.0900 82.0647 +0.0920 63.9564 +0.0940 41.5732 +0.0960 -114.408 +0.0980 -342.996 +0.1000 -289.586 +0.1020 234.269 +0.1040 1023.25 +0.1060 1617.73 +0.1080 1778.66 +0.1100 1502.41 +0.1120 939.611 +0.1140 235.798 +0.1160 -441.056 +0.1180 -924.133 +0.1200 -1084.76 +0.1220 -887.306 +0.1240 -645.618 +0.1260 98.3492 +0.1280 215.697 +0.1300 228.514 +0.1320 68.9249 +0.1340 -152.533 +0.1360 -314.056 +0.1380 -355.276 +0.1400 -259.327 +0.1420 62.6616 +0.1440 610.851 +0.1460 1166.95 +0.1480 1376.27 +0.1500 1070.22 +0.1520 453.658 +0.1540 -158.612 +0.1560 -587.625 +0.1580 -802.82 +0.1600 -742.418 +0.1620 -329.843 +0.1640 260.255 +0.1660 1563.85 +0.1680 2099.99 +0.1700 2283.79 +0.1720 1921.29 +0.1740 1159.2 +0.1760 121.866 +0.1780 -938.471 +0.1800 -1713.03 +0.1820 -1979.88 +0.1840 -1729.61 +0.1860 -1118.46 +0.1880 -373.46 +0.1900 343.756 +0.1920 888.764 +0.1940 1080.51 +0.1960 841.869 +0.1980 280.294 +0.2000 -318.095