Hello Amber experts,
I am using the ABMD “COM_DISTANCE” variable to pull two peptides apart and measure the free energy as a function of peptide distance. I have the ABMD split into four input files over 40 Angstroms. I have pasted the MDin and colvar instructions below for reference. My question is regarding the resulting data. At 40 Angstroms, the maximum distance, the free energy of some of my systems plummets. This data seems abnormal, so I was wondering if any of you have seen this before and if it is a sign of something wrong in my simulation. I’m not sure how I should interpret this since I am looking for the lowest point of free energy but a huge plummet from 39-40 Angstroms seems like unrealistic data. I greatly appreciate any help.
Thanks,
Kyle
ABMD instructions:
Input file for ABMD
&cntrl
imin = 0, irest = 0, igb = 0, dielc = 1.0,
ntx = 1, ntb = 1, ntt = 3, ntp = 0
temp0 = 310.0, tautp = 2.0,
tol = 0.00001, ntc = 2, ntf = 2, iwrap = 1
cut = 9.0, ibelly = 0, dt = 0.002, gamma_ln=1.0
ntpr = 5000,
ntwr = 5000,
ntwx = 5000,
nstlim = 25000000,
nscm = 100, infe = 1, ntwprt = 19,
ntr = 0, ipol = 0
&end
&abmd
mode = 'FLOODING'
timescale = 1.0
monitor_freq = 500
monitor_file = 'abmd_monitor_1.dat'
cv_file = 'cv.dist.in'
umbrella_file = 'bias_1.nc'
selection_freq = 5000
selection_constant = 0.00001
selection_epsilon = 0.0
wt_temperature = 10000
wt_umbrella_file = 'wt_bias_1.nc'
/
~
My colvar file is as follows: (the two peptides are divided after the 394th atom)
&colvar
npath = 2, nharm = 1,
path = 8.0, 5.0,
harm = 10.0
cv_type = 'COM_DISTANCE'
cv_min = 0.0, cv_max = 40.0, resolution = 1.0
cv_ni = 788,
cv_i = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394, 0, 395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788
/
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Received on Tue Oct 01 2019 - 14:30:02 PDT
