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

[Yang Ye]

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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