Glad it all worked out, I'm surprised that the old version didn't throw an
input read error for not recognizing ncsu in the old version, but oh well.
--Dan
On Sat, Oct 23, 2010 at 12:41 AM, <eduardo.troche.uvigo.es> wrote:
> Thank you Daniel, I was sending my jobs to a computational center and
> they were being done with a previous version of amber. I specified it
> and know everything is right and finally the smd.txt appeared!
>
> Daniel Sindhikara <sindhikara.gmail.com> escribiu:
>
> > 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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> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Dr. Daniel J. Sindhikara
> >> > Institute for Molecular Science
> >> > E-mail: sindhikara.gmail.com
> >> > Website: http://sites.google.com/site/dansindhikara/
> >> > --
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> >> > 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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> >
>
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>
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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 Sat Oct 23 2010 - 19:00:03 PDT
