Hi Feng
Thanks a lot (once again) for your help…
It turned out that the error was the final comma after each three coordinates in the cv_r lines… I first thought that deleting the comments may help (and it did) but further experiments showed that the problems were not the comments themself, but separating them with a comma before the “!”… After that it also worked with the extra “0” in the cv_ni line (I read in the nanual that it was optional… there is not any difference for including it, isn’t it?
Best
Lius
> On 29 May 2021, at 07:07, Feng Pan <fpan3.ncsu.edu> wrote:
>
> 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’ /
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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 Sat May 29 2021 - 06:00:02 PDT
