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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