Hi, Luis
Sounds good. It turns out that the COMMA confused the codes because it let
the code consider the "!..." comment to be some input.
This is definitely tricky and we should be careful.
The extra "0" should not have any problem even if there is only one group
of atoms, I was just not sure so ask you to try because it is long time
since I coded this, sorry for this.
Thank you for reporting this in the list.
Best
Feng
On Sat, May 29, 2021 at 8:36 AM Luis Simon <lsimon.usal.es> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> 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 - 12:00:02 PDT
