<div dir="ltr"> Just no reply from them for some time...<br>Thank you anyway.<br><br>Ye<br><div class="gmail_quote">2011/6/22 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;">
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.<u></u>html</a>, it is developped by Dr. Onuchic's group in UCSD.<br>
Has anyone used this?<br>
<br>
</blockquote>
<br></div>
Since this topology was not created by any standard Gromacs utility, wouldn't it be more efficient to contact the developers directly about implementation details and proper use?<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;"><div><div></div><div class="h5">
[ 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></div>
2011/6/22 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <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>
On 23/06/2011 10:36 AM, 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;">
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>
</blockquote>
<br>
The calculation uses the same algorithm and whatever values you<br>
input. Nowhere have you specified that these values are in anything<br>
other than the standard units, so how could GROMACS know to change<br>
anything? (Nor can you specify such)<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
But the calculation itself is different since the constants are<br>
different, so the result must differed a lot. Does gromacs knows<br>
that we are using reduced unit?<br>
</blockquote>
<br>
No. It's up to you to use a self-consistent set of input parameters,<br>
and to interpret the results correctly.<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2. With this program/forcefield to build top file automaticly,<br>
the KJ/mol it gives is in the top file, so it is still part of<br>
input, in this case , the gromacs will recognize it in the<br>
standard unit?<br>
</blockquote>
<br>
It doesn't recognize units. It follows an algorithm that is 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>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
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 author of the<br>
webtool emphasize that this structure based cg model is in reduced<br>
unit, so what result do I got?<br>
Has anyone used this webtool to do CG simulation and explain what<br>
is case?<br>
<br>
Thank you all very much.<br>
<br>
Ye<br>
<br></div></div>
2011/6/22 Yang Ye <<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>
<br>
Hi,<br>
<br>
The unit in output is in assumed to be for the standard unit<br>
input while the value is in reduced unit.<br>
<br>
So you need to do your own calculation to figure out 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></div><div><div></div><div class="h5">
<<a href="mailto:knightyangpku@gmail.com" target="_blank">knightyangpku@gmail.com</a> <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 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>
P25. On the contrary, if we use standard unit, the out<br>
put will be in standard unit.<br>
This brings the question up when we use 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>), according to the<br>
author, it seems that everything is in reduced unit, so<br>
the output file should also be in reduced unit, yet I<br>
found the topology file that the energy unit is KJ/mol.<br>
What exactly is the unit of the input and out put 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 compare<br>
with the experimental results, albeit the intrinsic<br>
difference. If I get something in reduced unit, there is<br>
necessity for me to change it into physical unit, or at<br>
least clarify it in comparison.<br>
Thank you very much.<br>
<br>
Ye<br>
<br>
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<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
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