If zero is your min, yes. But make sure the zero distance makes sense
in the structure conformation, means there is no atomic clashes.
Best
Feng
On Wed, Oct 2, 2019 at 11:41 AM Kyle Ghaby <ksg225.nau.edu> wrote:
> Hi Feng,
>
> Thank you for the reply. Is this expected to occur at 0 Angstroms as well?
>
> Thanks,
> Kyle
>
> > On Oct 2, 2019, at 8:17 AM, Feng Pan <fpan3.ncsu.edu> wrote:
> >
> > 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
> >> /
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> > Feng Pan
> > PostDoc
> > Florida State University
> > Department of Statistics
> > Email: fpan3.ncsu.edu; fpan.fsu.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
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Received on Thu Oct 03 2019 - 09:00:02 PDT
