I wonder, did you get an ncsu-smd.log file come out? I usually run abmd and
thus along
with my normal files, i automatically get a ncsu-abmd.log file describing
some of the parameters.
Is it possible that either you are running a version of amber without ncsu
(pre-amber 10) or
have it compiled without the ncsu package?
If you run the compile tests, does the ncsu part pass?
--Dan
On Fri, Oct 22, 2010 at 7:55 PM, <eduardo.troche.uvigo.es> wrote:
> You were right about ntwx, but I changed it and although the .mdcrd
> file appears, when you take a look at the trajectory, the system
> performed a normal MD simulation, without performing the SMD orders. I
> don't know if there is anything missing in the input file, both in
> mine and in the input from the manual, but is strange, since I have
> also used the file that appears in the test directory to run the same
> simulation, which has the same format as mine, and the same happened.
>
> Daniel Sindhikara <sindhikara.gmail.com> escribiu:
>
> > I've never run smd with the ncsu package but ntwx is the interval to
> write
> > crd files, you should probably bring that above zero.
> > Secondly, a small note, you should be careful to set your ig when you run
> > langevin dynamics (ntt=3).
> > Not sure about why the smd.txt isn't coming out.
> >
> > -Dan
> >
> > Monitoring steered molecular dynamics for the complex cydr_1
> >
> >> &cntrl
> >> igb = 0, ntx = 1,
> >> ntb = 0, ntp = 0, temp0 = 300.0,
> >> ntt = 3, gamma_ln = 1.0,
> >> ntf = 2, ntc = 2, tol = 0.00001,
> >> cut = 12.0, dt = 0.002,
> >> ntpr = 5, *ntwx = 0*, nstlim = 10000
> >> /
> >>
> >> ncsu_smd
> >>
> >> output_file = 'smd.txt'
> >> output_freq = 50
> >>
> >> variable
> >>
> >> path= (X, 6.0)
> >> harm = (10.0)
> >>
> >> type = DISTANCE
> >>
> >> #list of participating atoms
> >> i = (166, 92)
> >>
> >> #reference coordinates
> >> r = (-17.752, 5.695, -26.272, -17.216, 8.476, -25.557)
> >> end variable
> >>
> >> end ncsu_smd
> >>
> >>
> >> The problem is that i donīt get nor a mdcrd file, neither the smd.txt
> >> results file, so i don't really know what i'm doing wrong...I would
> >> appreciate any help you could give me.
> >>
> >> Thanks,
> >> Edu
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Fri Oct 22 2010 - 05:30:04 PDT
