<div dir="ltr">Thank you very much, Mark.<br><br>Is there anyway I can know the unit of input from the top file? I am not sure what I am getting from the webtool, although it shows "kj/mol" the instruction on the web says the unit is reduced unit, which makes me confused. In the former case I do not need to convert, but in latter case, I need to convert to standard units. The webtool is from <a href="http://smog.ucsd.edu/sbm_faq.html" target="_blank">http://smog.ucsd.edu/sbm_faq.html</a>, it is developped by Dr. Onuchic's group in UCSD.<br>
Has anyone used this?<br><br> <br>
[ angles ]<br>
;ai aj ak func th0(deg) Ka<br>
1 2 3 1 0.95664E+02 0.40000E+02<br>
2 3 4 1 0.91183E+02 0.40000E+02<br>
3 4 5 1 0.89842E+02 0.40000E+02<br>
4 5 6 1 0.91965E+02 0.40000E+02<br>
5 6 7 1 0.90670E+02 0.40000E+02<br>
6 7 8 1 0.91186E+02 0.40000E+02<br>
7 8 9 1 0.92703E+02 0.40000E+02<br>
8 9 10 1 0.91537E+02 0.40000E+02<br>
9 10 11 1 0.91328E+02 0.40000E+02<br>
10 11 12 1 0.92557E+02 0.40000E+02<br>
11 12 13 1 0.93372E+02 0.40000E+02<br>
12 13 14 1 0.94347E+02 0.40000E+02<br>
13 14 15 1 0.99411E+02 0.40000E+02<br>
14 15 16 1 0.98190E+02 0.40000E+02<br>
......<br>
[ dihedrals ]<br>
;ai aj ak al func phi0(deg) Kd(kJ/mol) mult<br>
1 2 3 4 1 0.24358E+03 0.10000E+01 1<br>
1 2 3 4 1 0.73074E+03 0.50000E+00 3<br>
2 3 4 5 1 0.22823E+03 0.10000E+01 1<br>
2 3 4 5 1 0.68469E+03 0.50000E+00 3<br>
3 4 5 6 1 0.23172E+03 0.10000E+01 1<br>
3 4 5 6 1 0.69515E+03 0.50000E+00 3<br>
4 5 6 7 1 0.22982E+03 0.10000E+01 1<br>
4 5 6 7 1 0.68946E+03 0.50000E+00 3<br>
<br><br>Thank you very much.<br><br>Ye <br><br><div class="gmail_quote">2011/6/22 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<u></u>
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 23/06/2011 10:36 AM, Ye Yang wrote:
<blockquote type="cite">
<div dir="ltr">Hi,<br>
Thanks for replying, Yang.<br>
But I still did not get it fully: <br>
1. So if we use reduced unit in input, the output and
calculation is still assumed to be in standard units?</div>
</blockquote>
<br></div>
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)<div class="im"><br>
<br>
<blockquote type="cite">
<div dir="ltr"> 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?<br>
</div>
</blockquote>
<br></div>
No. It's up to you to use a self-consistent set of input parameters,
and to interpret the results correctly.<div class="im"><br>
<br>
<blockquote type="cite">
<div dir="ltr">
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?<br>
</div>
</blockquote>
<br></div>
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 :-)<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<div dir="ltr"> 3. in the top file it gives:<br>
<br>
[ angles ]<br>
;ai aj ak func th0(deg) Ka<br>
1 2 3 1 0.95664E+02 0.40000E+02<br>
2 3 4 1 0.91183E+02 0.40000E+02<br>
3 4 5 1 0.89842E+02 0.40000E+02<br>
4 5 6 1 0.91965E+02 0.40000E+02<br>
5 6 7 1 0.90670E+02 0.40000E+02<br>
6 7 8 1 0.91186E+02 0.40000E+02<br>
7 8 9 1 0.92703E+02 0.40000E+02<br>
8 9 10 1 0.91537E+02 0.40000E+02<br>
9 10 11 1 0.91328E+02 0.40000E+02<br>
10 11 12 1 0.92557E+02 0.40000E+02<br>
11 12 13 1 0.93372E+02 0.40000E+02<br>
12 13 14 1 0.94347E+02 0.40000E+02<br>
13 14 15 1 0.99411E+02 0.40000E+02<br>
14 15 16 1 0.98190E+02 0.40000E+02<br>
......<br>
[ dihedrals ]<br>
;ai aj ak al func phi0(deg) Kd(kJ/mol) mult<br>
1 2 3 4 1 0.24358E+03 0.10000E+01 1<br>
1 2 3 4 1 0.73074E+03 0.50000E+00 3<br>
2 3 4 5 1 0.22823E+03 0.10000E+01 1<br>
2 3 4 5 1 0.68469E+03 0.50000E+00 3<br>
3 4 5 6 1 0.23172E+03 0.10000E+01 1<br>
3 4 5 6 1 0.69515E+03 0.50000E+00 3<br>
4 5 6 7 1 0.22982E+03 0.10000E+01 1<br>
4 5 6 7 1 0.68946E+03 0.50000E+00 3<br>
<br>
<br>
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? <br>
Has anyone used this webtool to do CG simulation and explain
what is case?<br>
<br>
Thank you all very much.<br>
<br>
Ye<br>
<br>
<div class="gmail_quote">2011/6/22 Yang Ye <span dir="ltr"><<a href="mailto:leafyoung@yahoo.com" target="_blank">leafyoung@yahoo.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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">
<div>
<div>On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang
<span dir="ltr"><<a href="mailto:knightyangpku@gmail.com" target="_blank">knightyangpku@gmail.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<div>
<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>
</div>
</div>
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