Hi, Kyle
This is an internal problem for ABMD, it will have some abnormal activity
near the boundary,
so just ignore it, you can count the relative free energy from the normal
region, like 38 or so.
If you really need the the free energy around 40, set to a larger upper
limit.
Best
Feng
On Tue, Oct 1, 2019 at 5:18 PM Kyle Ghaby <ksg225.nau.edu> wrote:
> 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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>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
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Received on Wed Oct 02 2019 - 08:30:02 PDT
