By fall out of use, you mean that the users are not asking questions
about it? Or do you mean to say that it is not a tool that amber
consider to be important anymore, and so it is doomed to disappear
from future amber releases? Or even that there are better ways in
amber to obtain free energies with regard to pulling processes?
Best regards
Fabrício
2012/8/27 Brian Radak <radak004.umn.edu>:
> Hi Fabricio,
>
> Unfortunately the ncsu modules are beginning to fall out of use these days.
> I have not seen many regular users post on this list in quite some time,
> especially with regards to the abmd module. I can only suggest looking at
> the source code. I'm sorry I can't offer any more information than that.
>
> Regards,
> Brian
>
> On Mon, Aug 27, 2012 at 11:17 AM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
>
>> Hi. I am sorry to resend this, but I just want to make sure that you
>> guys received the email. I am worried because I had already two other
>> threads on the mail list and I don't know if things get mixed up or
>> not. So, again, I am sorry if this causes any inconvenience, but I
>> just wanted to make sure.
>> Thank you
>> Fabrício
>>
>> Hello Amber folks.
>> Is it possible to use the LCOD variable with ncsu_abmd? If so, are the
>> min and max variables required?
>>
>> Secondly. I am having some trouble with the mdin file for the
>> ncsu_abmd simulation. My file goes like this:
>> Parameters for qmmm md run
>> &cntrl
>> .....parameters for md simulation...
>> /
>> &qmmm
>> ......parameters for the qmmm part.....
>> /
>> ncsu_abmd
>> mode=FLOODING
>> monitor_file='abmd.txt'
>> monitor_freq=50
>> timescale=10.0
>> .....and the rest of the variables (this is what the first two
>> questions of the email adress)
>>
>> Once I run sander, the following error show up on the mdout file.
>> ** NCSU-Error ** : 'md_qmmm.in', line:25, col:1 : unexpected character
>>
>> Line 25 is the that specifies: ncsu_abmd
>>
>> Any help here would be great
>> Thank you
>> Fabrício Bracht
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ================================ Current Address =======================
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Received on Mon Aug 27 2012 - 11:00:04 PDT
