<div dir="ltr">Thank you very much!<br>I will check with them carefully.<br><br>Ye<br><br><div class="gmail_quote">2011/6/23 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;"><div class="im"><br>
<br>
Ye Yang wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Just no reply from them for some time...<br>
</blockquote>
<br></div>
Well, that's unfortunate. I'd hazard a guess that all the units are reduced, but that's just a hunch. Theoretically, all your input and output should be in reduced units. My hunch is based on the fact that everything shown (in terms of force constants) is a nice, round number (5, 10, 400) which seems odd for standard values (see any ffbonded.itp for "normal" values). It looks like everything is relative to the reduced units, but to be sure you'd really have to get a response from those who developed the web service you're trying to use, if this information is not otherwise documented somewhere (FAQ's, publication, etc).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you anyway.<br>
<br>
Ye<br>
2011/6/22 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><div></div><div class="h5"><br>
<br>
<br>
<br>
Ye Yang wrote:<br>
<br>
Thank you very much, Mark.<br>
<br>
Is there anyway I can know the unit of input from the top file?<br>
I am not sure what I am getting from the webtool, although it<br>
shows "kj/mol" the instruction on the web says the unit is<br>
reduced unit, which makes me confused. In the former case I do<br>
not need to convert, but in latter case, I need to convert to<br>
standard units. The webtool is from<br>
<a href="http://smog.ucsd.edu/sbm_faq.__html" target="_blank">http://smog.ucsd.edu/sbm_faq._<u></u>_html</a><br>
<<a href="http://smog.ucsd.edu/sbm_faq.html" target="_blank">http://smog.ucsd.edu/sbm_faq.<u></u>html</a>>, it is developped by Dr.<br>
Onuchic's group in UCSD.<br>
Has anyone used this?<br>
<br>
<br>
Since this topology was not created by any standard Gromacs utility,<br>
wouldn't it be more efficient to contact the developers directly<br>
about implementation details and proper use?<br>
<br>
-Justin<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>
2011/6/22 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>><br></div></div>
<mailto:<a href="mailto:Mark.Abraham@anu.edu." target="_blank">Mark.Abraham@anu.edu.</a>_<u></u>_au <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>>><div>
<div></div><div class="h5"><br>
<br>
<br>
__<br>
On 23/06/2011 10:36 AM, Ye Yang wrote:<br>
<br>
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<br>
calculation is still assumed to be in standard units?<br>
<br>
<br>
The calculation uses the same algorithm and whatever values you<br>
input. Nowhere have you specified that these values are in<br>
anything<br>
other than the standard units, so how could GROMACS know to<br>
change<br>
anything? (Nor can you specify such)<br>
<br>
<br>
But the calculation itself is different since the<br>
constants are<br>
different, so the result must differed a lot. Does<br>
gromacs knows<br>
that we are using reduced unit?<br>
<br>
<br>
No. It's up to you to use a self-consistent set of input<br>
parameters,<br>
and to interpret the results correctly.<br>
<br>
<br>
2. With this program/forcefield to build top file<br>
automaticly,<br>
the KJ/mol it gives is in the top file, so it is still<br>
part of<br>
input, in this case , the gromacs will recognize it in the<br>
standard unit?<br>
<br>
<br>
It doesn't recognize units. It follows an algorithm that is<br>
correct<br>
if all the quantities are measured in the standard units. If you<br>
change something, you have to understand all the consequences and<br>
interpret appropriately :-)<br>
<br>
Mark<br>
<br>
<br>
3. in the top file it gives:<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<br>
author of the<br>
webtool emphasize that this structure based cg model is<br>
in reduced<br>
unit, so what result do I got?<br>
Has anyone used this webtool to do CG simulation and<br>
explain what<br>
is case?<br>
<br>
Thank you all very much.<br>
<br>
Ye<br>
<br>
2011/6/22 Yang Ye <<a href="mailto:leafyoung@yahoo.com" target="_blank">leafyoung@yahoo.com</a><br></div></div>
<mailto:<a href="mailto:leafyoung@yahoo.com" target="_blank">leafyoung@yahoo.com</a>> <mailto:<a href="mailto:leafyoung@yahoo.com" target="_blank">leafyoung@yahoo.com</a><div class="im"><br>
<mailto:<a href="mailto:leafyoung@yahoo.com" target="_blank">leafyoung@yahoo.com</a>>>><br>
<br>
<br>
Hi,<br>
<br>
The unit in output is in assumed to be for the<br>
standard unit<br>
input while the value is in reduced unit.<br>
<br>
So you need to do your own calculation to figure out<br>
what's<br>
the reduced unit is.<br>
<br>
Regards,<br>
Yang Ye<br>
<br>
On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang<br>
<<a href="mailto:knightyangpku@gmail.com" target="_blank">knightyangpku@gmail.com</a><br>
<mailto:<a href="mailto:knightyangpku@gmail.com" target="_blank">knightyangpku@gmail.<u></u>com</a>><br></div>
<mailto:<a href="mailto:knightyangpku@gmail." target="_blank">knightyangpku@gmail.</a>__<u></u>com<div><div></div><div class="h5"><br>
<mailto:<a href="mailto:knightyangpku@gmail.com" target="_blank">knightyangpku@gmail.<u></u>com</a>>>> wrote:<br>
<br>
Dear all:<br>
I see from the user's manual that if our<br>
input is<br>
in reduced unit, the output will also be in reduced<br>
unit(,<a href="ftp://ftp.gromacs.org/__pub/manual/3.1/manual-a4-3.1.__1.pdf" target="_blank">ftp://ftp.gromacs.org/__<u></u>pub/manual/3.1/manual-a4-3.1._<u></u>_1.pdf</a><br>
<<a href="ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf" target="_blank">ftp://ftp.gromacs.org/pub/<u></u>manual/3.1/manual-a4-3.1.1.pdf</a><u></u>>),<br>
P25. On the contrary, if we use standard unit,<br>
the out<br>
put will be in standard unit.<br>
This brings the question up when we use<br>
coarse<br>
grain Clementi's model webtool<br>
(<a href="http://smog.ucsd.edu/sbm_faq.__html" target="_blank">http://smog.ucsd.edu/sbm_faq.<u></u>__html</a><br>
<<a href="http://smog.ucsd.edu/sbm_faq.html" target="_blank">http://smog.ucsd.edu/sbm_faq.<u></u>html</a>>), according to the<br>
author, it seems that everything is in reduced<br>
unit, so<br>
the output file should also be in reduced unit, yet I<br>
found the topology file that the energy unit is<br>
KJ/mol.<br>
What exactly is the unit of the input and out put<br>
file?<br>
When I pull the molecules, do I get the reduced unit<br>
result or the physical unit result?<br>
Since I am an experimentalist, getting the<br>
physical units is more important to me, so as to<br>
compare<br>
with the experimental results, albeit the intrinsic<br>
difference. If I get something in reduced unit,<br>
there is<br>
necessity for me to change it into physical unit,<br>
or at<br>
least clarify it in comparison.<br>
Thank you very much.<br>
<br>
Ye<br>
<br>
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