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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 23 03:46:05 CEST 2011 

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>> 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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