Re: [AMBER] ABMD COM_DISTANCE Help

From: Feng Pan <fpan3.ncsu.edu>
Date: Thu, 3 Oct 2019 13:26:37 -0400

0 A means the value of the reaction coordinate you defined is zero.

Feng

On Thu, Oct 3, 2019 at 12:17 PM Kyle Ghaby <ksg225.nau.edu> wrote:

> Does 0 A mean 0 A apart or 0 A from the initial conformation?
>
> Thanks,
> Kyle
>
> > On Oct 3, 2019, at 8:57 AM, Feng Pan <fpan3.ncsu.edu> wrote:
> >
> > 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
> > _______________________________________________
> > 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 - 10:30:02 PDT
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