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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Received on Fri Oct 22 2010 - 04:00:04 PDT
