[gmx-users]Question about reduced unit for coarse grain
Ye Yang
knightyangpku at gmail.com
Thu Jun 23 06:19:39 CEST 2011
Just no reply from them for some time...
Thank you anyway.
Ye
2011/6/22 Justin A. Lemkul <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>,
>> 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>>>
>>
>>
>> __
>> 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>>
>>>
>>>
>>> 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>>>
>>> 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>),
>>> 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>),
>>> 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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>>
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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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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