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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>> >> 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/
>> > --
>> > _______________________________________________
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>> > 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 - 09:00:05 PDT
