[gmx-users]Question about reduced unit for coarse grain

[Ye Yang]

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? 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?
    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?
    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>

> 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> 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), 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), 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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