The cv_ni and cv_nr should be defined explicitly or it will use the default
value zero, and leads to the error,
so just add
cv_nr=1, cv_ni =16 (since you have 16 atoms included)
to the &colvar section.
Feng
On Sun, Nov 3, 2019 at 9:48 AM Federico Iacovelli <
federico.iacovelli.uniroma2.it> wrote:
> Dear all,
>
> I'm trying to setup an ABMD simulation of my system using two
> reaction coordinates. While the DISTANCE cv works fine, I'm experiencing
> a weird problem with the N_OF_BONDS cv. pmemd returns this error:
>
> ** NFE-Error ** : number of elements in cv_i array must be positive!
>
> As you can see my array is populated...
>
> This is my input file:
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 7,
> infe = 1,
> ntb = 2, pres0 = 1.0, ntp =1 , taup= 2.0
> cut = 8.0, iwrap = 1,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 25000000, dt = 0.002
> ntpr = 1000, ntwx = 1000, ntwr = 1000, ioutfm = 1
> /
>
> &abmd
> mode = 'FLOODING'
> timescale = 1.0,
> monitor_file = 'abmd_monitor_1.dat',
> monitor_freq = 100, ! 10 ps
> umbrella_file = 'bias_1.nc',
> cv_file = 'cv_test.in'
> /
>
>
> My colvar file is as follows:
> &colvar
> cv_type = 'N_OF_BONDS',
> cv_r = 2.50,
> cv_i = 17, 977, 49, 1009, 114, 1071, 146, 1103, 178, 1135, 210,
> 1167, 275, 1229, 307, 1261
> cv_min = 0.0,
> cv_max = 12.0,
> resolution = 0.2
>
> /
>
> Thanks for your help
>
> F.I.
>
> _______________________________________________
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> 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 Sun Nov 03 2019 - 12:00:02 PST
