[gmx-users]Question about reduced unit for coarse grain
Ye Yang
knightyangpku at gmail.com
Thu Jun 23 06:27:10 CEST 2011
Thank you very much!
I will check with them carefully.
Ye
2011/6/23 Justin A. Lemkul <jalemkul at vt.edu>
>
>
> Ye Yang wrote:
>
>> Just no reply from them for some time...
>>
>
> Well, that's unfortunate. I'd hazard a guess that all the units are
> reduced, but that's just a hunch. Theoretically, all your input and output
> should be in reduced units. My hunch is based on the fact that everything
> shown (in terms of force constants) is a nice, round number (5, 10, 400)
> which seems odd for standard values (see any ffbonded.itp for "normal"
> values). It looks like everything is relative to the reduced units, but to
> be sure you'd really have to get a response from those who developed the web
> service you're trying to use, if this information is not otherwise
> documented somewhere (FAQ's, publication, etc).
>
> -Justin
>
> Thank you anyway.
>>
>> Ye
>> 2011/6/22 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>>
>> Ye Yang wrote:
>>
>> Thank you very much, Mark.
>>
>> Is there anyway I can know the unit of input from the top file?
>> I am not sure what I am getting from the webtool, although it
>> shows "kj/mol" the instruction on the web says the unit is
>> reduced unit, which makes me confused. In the former case I do
>> not need to convert, but in latter case, I need to convert to
>> standard units. The webtool is from
>> http://smog.ucsd.edu/sbm_faq._**_html<http://smog.ucsd.edu/sbm_faq.__html>
>> <http://smog.ucsd.edu/sbm_faq.**html<http://smog.ucsd.edu/sbm_faq.html>>,
>> it is developped by Dr.
>> Onuchic's group in UCSD.
>> Has anyone used this?
>>
>>
>> Since this topology was not created by any standard Gromacs utility,
>> wouldn't it be more efficient to contact the developers directly
>> about implementation details and proper use?
>>
>> -Justin
>>
>> [ angles ]
>> ;ai aj ak func th0(deg) Ka
>> 1 2 3 1 0.95664E+02 0.40000E+02
>> 2 3 4 1 0.91183E+02 0.40000E+02
>> 3 4 5 1 0.89842E+02 0.40000E+02
>> 4 5 6 1 0.91965E+02 0.40000E+02
>> 5 6 7 1 0.90670E+02 0.40000E+02
>> 6 7 8 1 0.91186E+02 0.40000E+02
>> 7 8 9 1 0.92703E+02 0.40000E+02
>> 8 9 10 1 0.91537E+02 0.40000E+02
>> 9 10 11 1 0.91328E+02 0.40000E+02
>> 10 11 12 1 0.92557E+02 0.40000E+02
>> 11 12 13 1 0.93372E+02 0.40000E+02
>> 12 13 14 1 0.94347E+02 0.40000E+02
>> 13 14 15 1 0.99411E+02 0.40000E+02
>> 14 15 16 1 0.98190E+02 0.40000E+02
>> ......
>> [ dihedrals ]
>> ;ai aj ak al func phi0(deg) Kd(kJ/mol) mult
>> 1 2 3 4 1 0.24358E+03 0.10000E+01 1
>> 1 2 3 4 1 0.73074E+03 0.50000E+00 3
>> 2 3 4 5 1 0.22823E+03 0.10000E+01 1
>> 2 3 4 5 1 0.68469E+03 0.50000E+00 3
>> 3 4 5 6 1 0.23172E+03 0.10000E+01 1
>> 3 4 5 6 1 0.69515E+03 0.50000E+00 3
>> 4 5 6 7 1 0.22982E+03 0.10000E+01 1
>> 4 5 6 7 1 0.68946E+03 0.50000E+00 3
>>
>>
>> Thank you very much.
>>
>> Ye
>>
>> 2011/6/22 Mark Abraham <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.**au <Mark.Abraham at anu.edu.au>>
>> <mailto:Mark.Abraham at anu.edu._**_au <mailto:Mark.Abraham at anu.edu.*
>> *au <Mark.Abraham at anu.edu.au>>>>
>>
>>
>>
>> __
>> On 23/06/2011 10:36 AM, Ye Yang wrote:
>>
>> Hi,
>> Thanks for replying, Yang.
>> But I still did not get it fully:
>> 1. So if we use reduced unit in input, the output and
>> calculation is still assumed to be in standard units?
>>
>>
>> The calculation uses the same algorithm and whatever values you
>> input. Nowhere have you specified that these values are in
>> anything
>> other than the standard units, so how could GROMACS know to
>> change
>> anything? (Nor can you specify such)
>>
>>
>> But the calculation itself is different since the
>> constants are
>> different, so the result must differed a lot. Does
>> gromacs knows
>> that we are using reduced unit?
>>
>>
>> No. It's up to you to use a self-consistent set of input
>> parameters,
>> and to interpret the results correctly.
>>
>>
>> 2. With this program/forcefield to build top file
>> automaticly,
>> the KJ/mol it gives is in the top file, so it is still
>> part of
>> input, in this case , the gromacs will recognize it in the
>> standard unit?
>>
>>
>> It doesn't recognize units. It follows an algorithm that is
>> correct
>> if all the quantities are measured in the standard units. If you
>> change something, you have to understand all the consequences
>> and
>> interpret appropriately :-)
>>
>> Mark
>>
>>
>> 3. in the top file it gives:
>> [ angles ]
>> ;ai aj ak func th0(deg) Ka
>> 1 2 3 1 0.95664E+02 0.40000E+02
>> 2 3 4 1 0.91183E+02 0.40000E+02
>> 3 4 5 1 0.89842E+02 0.40000E+02
>> 4 5 6 1 0.91965E+02 0.40000E+02
>> 5 6 7 1 0.90670E+02 0.40000E+02
>> 6 7 8 1 0.91186E+02 0.40000E+02
>> 7 8 9 1 0.92703E+02 0.40000E+02
>> 8 9 10 1 0.91537E+02 0.40000E+02
>> 9 10 11 1 0.91328E+02 0.40000E+02
>> 10 11 12 1 0.92557E+02 0.40000E+02
>> 11 12 13 1 0.93372E+02 0.40000E+02
>> 12 13 14 1 0.94347E+02 0.40000E+02
>> 13 14 15 1 0.99411E+02 0.40000E+02
>> 14 15 16 1 0.98190E+02 0.40000E+02
>> ......
>> [ dihedrals ]
>> ;ai aj ak al func phi0(deg) Kd(kJ/mol) mult
>> 1 2 3 4 1 0.24358E+03 0.10000E+01 1
>> 1 2 3 4 1 0.73074E+03 0.50000E+00 3
>> 2 3 4 5 1 0.22823E+03 0.10000E+01 1
>> 2 3 4 5 1 0.68469E+03 0.50000E+00 3
>> 3 4 5 6 1 0.23172E+03 0.10000E+01 1
>> 3 4 5 6 1 0.69515E+03 0.50000E+00 3
>> 4 5 6 7 1 0.22982E+03 0.10000E+01 1
>> 4 5 6 7 1 0.68946E+03 0.50000E+00 3
>>
>>
>> Seems to me that this is the standard unit, yet the
>> author of the
>> webtool emphasize that this structure based cg model is
>> in reduced
>> unit, so what result do I got?
>> Has anyone used this webtool to do CG simulation and
>> explain what
>> is case?
>>
>> Thank you all very much.
>>
>> Ye
>>
>> 2011/6/22 Yang Ye <leafyoung at yahoo.com
>> <mailto:leafyoung at yahoo.com> <mailto:leafyoung at yahoo.com
>>
>> <mailto:leafyoung at yahoo.com>>>
>>
>>
>> Hi,
>>
>> The unit in output is in assumed to be for the
>> standard unit
>> input while the value is in reduced unit.
>>
>> So you need to do your own calculation to figure out
>> what's
>> the reduced unit is.
>>
>> Regards,
>> Yang Ye
>>
>> On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang
>> <knightyangpku at gmail.com
>> <mailto:knightyangpku at gmail.**com <knightyangpku at gmail.com>>
>> <mailto:knightyangpku at gmail.__**com
>>
>> <mailto:knightyangpku at gmail.**com <knightyangpku at gmail.com>>>>
>> wrote:
>>
>> Dear all:
>> I see from the user's manual that if our
>> input is
>> in reduced unit, the output will also be in reduced
>> unit(,ftp://ftp.gromacs.org/__**
>> pub/manual/3.1/manual-a4-3.1._**_1.pdf<ftp://ftp.gromacs.org/__pub/manual/3.1/manual-a4-3.1.__1.pdf>
>> <ftp://ftp.gromacs.org/pub/**manual/3.1/manual-a4-3.1.1.pdf<ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf>
>> **>),
>> P25. On the contrary, if we use standard unit,
>> the out
>> put will be in standard unit.
>> This brings the question up when we use
>> coarse
>> grain Clementi's model webtool
>> (http://smog.ucsd.edu/sbm_faq.**__html<http://smog.ucsd.edu/sbm_faq.__html>
>> <http://smog.ucsd.edu/sbm_faq.**html<http://smog.ucsd.edu/sbm_faq.html>>),
>> according to the
>> author, it seems that everything is in reduced
>> unit, so
>> the output file should also be in reduced unit, yet
>> I
>> found the topology file that the energy unit is
>> KJ/mol.
>> What exactly is the unit of the input and out put
>> file?
>> When I pull the molecules, do I get the reduced unit
>> result or the physical unit result?
>> Since I am an experimentalist, getting the
>> physical units is more important to me, so as to
>> compare
>> with the experimental results, albeit the intrinsic
>> difference. If I get something in reduced unit,
>> there is
>> necessity for me to change it into physical unit,
>> or at
>> least clarify it in comparison.
>> Thank you very much.
>>
>> Ye
>>
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>> -- ==============================**__==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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