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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