<div>Hi,<br clear="all"></div><div><br></div><div>The unit in output is in assumed to be for the standard unit input while the value is in reduced unit.</div><div><br></div><div>So you need to do your own calculation to figure out what's the reduced unit is.</div>
<div><br></div>Regards,<br>Yang Ye<br>
<br><div class="gmail_quote">On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang <span dir="ltr"><<a href="mailto:knightyangpku@gmail.com">knightyangpku@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div dir="ltr">Dear all:<br> I see from the user's manual that if our input is in reduced unit, the output will also be in reduced unit(,<a href="ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf" target="_blank">ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf</a>), P25. On the contrary, if we use standard unit, the out put will be in standard unit.<br>
This brings the question up when we use coarse grain Clementi's model webtool (<a href="http://smog.ucsd.edu/sbm_faq.html" target="_blank">http://smog.ucsd.edu/sbm_faq.html</a>), 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?<br>
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.<br>
Thank you very much.<br><br>Ye<br></div>
<br>--<br>
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