Hi, Ruth
For the newest &smd, you can not use X to indicate the initial value of CV,
you need to give the initial value explicitly.
Feng
On Wed, Dec 7, 2016 at 1:08 PM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
>
> Dear Dan,
>
> Unfortunately, I've tried with a comma after it but I'm still getting the
> same error message.. I've also added commas in the &smd section but I'm
> getting the same.
>
> Thank you anyway for your suggestion.
> Sincerely,
>
> Ruth
>
>
> On Wednesday, December 07, 2016 16:07 CET, Daniel Roe <
> daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Seems like you might be missing a comma after
>
> cv_type = 'LCOD'
>
> in the colvar namelist.
>
> -Dan
>
> On Wed, Dec 7, 2016 at 7:32 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
> wrote:
> > Dear amber users,
> >
> > I’ve been running SMD for my protein and its ligand in explicit solvent
> using LCOD.
> > In order to start the steering at the right value, I’d like to put an
> “X” as the beginning value of the steering path. In order to see if this
> feature is still working, I’ve tried first on A10 tutorial and, although
> I’ve run it several times, I get this odd error message that I didn’t get
> before (even when I remove the “X” and I try to re-run with a value of 0.7):
> >
> > ** NFE-Error ** : Cannot read &colvar namelist!
> >
> > I’ve double checked and the cv.in file is in the directory:
> >
> > sandiego:Athena rhtichau$ ls
> > cv.in mr_pd-10-500.rst mr_pd-20-10.out smd.txt
> > mdin mr_pd-10.nc mr_pd-50.nc smd_10-50.txt
> > mdinfo mr_pd-10.out mr_pd-50.out smd_10-500.txt
> > mr_pd-10-50.nc mr_pd-10.rst mr_pd-50.rst smd_10.txt
> > mr_pd-10-50.out mr_pd-100.nc mr_pd.nc smd_100.txt
> > mr_pd-10-50.rst mr_pd-100.out mr_pd.out smd_50.txt
> > mr_pd-10-500.nc mr_pd-100.rst mr_pd.rst test_harm-outputfreq
> > mr_pd-10-500.out mr_pd-20-10.nc qmmm_region.pdb
> >
> > I guess it’s some very silly mistake and yet I can’t see it. Please help
> me find it. Following are the input and the cv.in files:
> >
> > Malonaldehyde: NCSU steered MD: LCOD rxn coord
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 0,
> > cut = 999.0,
> > tempi = 300.0,
> > temp0 = 300.0,
> > ntt = 3,
> > gamma_ln = 1.0,
> > ntf = 2, ntc = 2, tol = 0.00001,
> > dt = 0.0005,
> > ntpr = 50, ntwr=100, ntwx = 100,
> > nstlim = 100000,
> > ifqnt = 1, infe=1,
> > /
> > &qmmm
> > qmmask=':*',
> > qmcharge=0,
> > qm_theory='PM3',
> > qmshake=0,
> > writepdb=1,
> > /
> > &smd
> > output_file = 'smd_20-10.txt'
> > output_freq = 10
> > cv_file='cv.in'
> > /
> >
> >
> > &colvar
> > cv_type = 'LCOD'
> > cv_ni=4, cv_i = 8,9,7,9,
> > cv_nr=2, cv_r = 1.0,-1.0,
> > npath =2, path = X,-0.7,
> > nharm=1, harm = 20.0
> > /
> >
> > I tried to run the calculation with the following command:
> >
> > $AMBERHOME/bin/sander -i mdin -p ../../01/mr.top -c ../../01/mr_eq.rst
> -o mr_pd-20-10.out -r mr_pd-20-10.rst -x mr_pd-20-10.nc
> >
> > Thanks in advance for any suggestion,
> >
> > Ruth
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
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>
>
>
>
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>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Wed Dec 07 2016 - 10:30:03 PST
