Hi, Luis Simon
Try to remove the last ZERO in cv_i and change cv_ni to 10.
Best
Feng
On Mon, May 24, 2021 at 6:39 AM Luis Simon <lsimon.usal.es> wrote:
> I am trying to run a SMD calculation using NFE with a “MULTI_RMSD”
> colective variable using the following colvar input:
>
>
> &colvar
> cv_type = 'MULTI_RMSD',
> cv_ni = 11, cv_i = 156, 157, 158, 153, 159, 816, 812, 818, 837, 835,
> 0,
> cv_nr = 30,
> cv_r = -5.6128, -7.2523, 6.1539, !atom :6.P
> -5.0432, -7.6477, 6.5182, !atom :6.OP1
> -6.7184, -7.3110, 6.6237, !atom :6.OP2
> -5.2068, -9.2278, 5.3385, !atom :5.O2'
> -5.8180, -6.3964, 6.3792, !atom :6.O5'
> -11.4732, -3.3420, 12.0481, !atom :24.NN18
> -12.3551, -2.2275, 11.7429, !atom :24.PN14
> -12.8224, -2.6755, 11.1650, !atom :24.NN20
> -11.5725, -5.5491, 13.8352, !atom :24.NN39
> -12.0094, -3.4476, 8.9351, !atom :24.NN37
> npath = 2, path = 1.9538, 0.0, path_mode = 'LINES', nharm = 1,
> harm = 80.0000,
>
> /
>
> However, the output file complains of an error in the colvar namelist:
>
> ** NFE-Error ** : Cannot read &colvar namelist!
>
> Where is my mistake? is it not possible to use SMD with MULTI_RMSD
> variable? (the goal of the calculation is to gradually move the atoms of a
> system until they match to the positions defined in the cv_r list, hence
> the final “0.0” value in the path; the initial path value corresponds to
> the initial structure RMSD)
>
> Thanks in advanced:
>
> Luis Simón
>
> (the amber input file contains the following lines for requesting smd)
> &smd
> output_file = 'smd.txt'
> output_freq = 200
> cv_file = 'smd_cv.001.in’ /
>
>
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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 Fri May 28 2021 - 22:30:02 PDT
