[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
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>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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