Ooops... thank you Feng!
On Wed, 22 Jul 2020 21:21:51 -0400
Feng Pan <fpan3.ncsu.edu> wrote:
> 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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>> 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 Jul 23 2020 - 08:30:03 PDT
