[AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist!

From: Diego Morone <diego.morone.irb.usi.ch>
Date: Mon, 20 Jul 2020 15:37:31 +0200

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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Received on Mon Jul 20 2020 - 07:00:03 PDT
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