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
