Hi, Diego
It should be cv_ni instead of cv_i in the R_OF_GYRATION
Feng
On Mon, Jul 20, 2020 at 9:38 AM Diego Morone <diego.morone.irb.usi.ch>
wrote:
> Dear AMBER users,
>
> I am trying to get ABMD working with MULTI_RMSD and R_OF_GYRATION
> collective
> variables. My test protein is trp-cage and I would like to use the RMSD
> and
> RoG of CA atoms. However, I get an error
> ** NFE-Error ** : Cannot read &colvar namelist!
>
> With the 'COM_TORSION' variables I can everything running nice and smooth
> but not with these two. Do you have any suggestions?
>
> Here's my input cv and mdin files
>
> Many thanks
> Diego
>
> cv.in:
>
> &colvar
> cv_type = 'MULTI_RMSD',
> cv_ni = 21,
> cv_nr = 60,
> cv_i =
> 5,19,38,59,78,95,119,138,160,172,179,194,200,211,222,229,261,275,289,295,0,
>
> cv_r = 25.42533175,22.31146730,14.64956477, ! atom 5
> 26.86925550,23.52779165,17.98268164, ! atom 19
> 27.76566306,21.49552840,21.07471035, ! atom 38
> 24.64309980,19.37704464,21.60032528, ! atom 59
> 24.36150789,18.24989885,17.83645201, ! atom 78
> 28.19620357,17.69256331,17.74501671, ! atom 95
> 27.73690272,15.27400886,20.75363925, ! atom 119
> 24.86157939,13.60680882,18.76692841, ! atom 138
> 27.41439796,13.32391568,15.85196731, ! atom 160
> 29.92431910,11.51583512,18.29256757, ! atom 172
> 31.72581794,14.26850435,20.26027144, ! atom 179
> 35.46889916,13.91546659,19.89235379, ! atom 194
> 35.05320929,10.99977191,17.42466768, ! atom 200
> 32.99878035,13.20919701,14.96132667, ! atom 211
> 36.17109382,14.29100920,13.09605324, ! atom 222
> 35.95747845,18.07260037,13.41775957, ! atom 229
> 35.06762381,21.16730798,15.67273509, ! atom 261
> 31.38109091,22.24372320,16.21432248, ! atom 275
> 29.98699372,23.42798240,12.85646922, ! atom 289
> 27.90230178,26.62432877,13.01403142, ! atom 295
>
> resolution = 0.2,
> /
>
> &colvar
> cv_type = 'R_OF_GYRATION',
> cv_n = 20,
> cv_i =
> 5,19,38,59,78,95,119,138,160,172,179,194,200,211,222,229,261,275,289,295,
> resolution = 0.2,
> /
>
> mdin:
>
> Input file for ABMD
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> iwrap = 1,
> cut = 9.0,
> nstlim = 25000000,
> ntt = 3,
> temp0 = 300.0,
> gamma_ln=1.0,
> ntc = 2,
> ntf = 2,
> tol = 0.00001,
> dt = 0.002,
> ntpr = 5000,
> ntwr = 5000,
> ntwx = 5000,
> nscm = 100,
> infe = 1,
> ntwprt = 305
> &end
>
> &abmd
> mode = 'FLOODING',
> timescale = 1.0,
> monitor_file = 'abmd_monitor_1.dat',
> monitor_freq = 500,
> cv_file = 'cv.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',
> /
>
>
>
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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 Jul 22 2020 - 18:30:03 PDT
