Ye Yang wrote:
Just no reply from them for some time...
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).
-Justin
Thank you anyway.
Ye
2011/6/22 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Ye Yang wrote:
Thank you very much, Mark.
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
http://smog.ucsd.edu/sbm_faq.__html
<http://smog.ucsd.edu/sbm_faq.html>, it is developped by Dr.
Onuchic's group in UCSD.
Has anyone used this?
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?
-Justin
[ angles ]
;ai aj ak func th0(deg) Ka
1 2 3 1 0.95664E+02 0.40000E+02
2 3 4 1 0.91183E+02 0.40000E+02
3 4 5 1 0.89842E+02 0.40000E+02
4 5 6 1 0.91965E+02 0.40000E+02
5 6 7 1 0.90670E+02 0.40000E+02
6 7 8 1 0.91186E+02 0.40000E+02
7 8 9 1 0.92703E+02 0.40000E+02
8 9 10 1 0.91537E+02 0.40000E+02
9 10 11 1 0.91328E+02 0.40000E+02
10 11 12 1 0.92557E+02 0.40000E+02
11 12 13 1 0.93372E+02 0.40000E+02
12 13 14 1 0.94347E+02 0.40000E+02
13 14 15 1 0.99411E+02 0.40000E+02
14 15 16 1 0.98190E+02 0.40000E+02
......
[ dihedrals ]
;ai aj ak al func phi0(deg) Kd(kJ/mol) mult
1 2 3 4 1 0.24358E+03 0.10000E+01 1
1 2 3 4 1 0.73074E+03 0.50000E+00 3
2 3 4 5 1 0.22823E+03 0.10000E+01 1
2 3 4 5 1 0.68469E+03 0.50000E+00 3
3 4 5 6 1 0.23172E+03 0.10000E+01 1
3 4 5 6 1 0.69515E+03 0.50000E+00 3
4 5 6 7 1 0.22982E+03 0.10000E+01 1
4 5 6 7 1 0.68946E+03 0.50000E+00 3
Thank you very much.
Ye
2011/6/22 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au <mailto:mark.abra...@anu.edu.au>>>
__
On 23/06/2011 10:36 AM, Ye Yang wrote:
Hi,
Thanks for replying, Yang.
But I still did not get it fully:
1. So if we use reduced unit in input, the output and
calculation is still assumed to be in standard units?
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)
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?
No. It's up to you to use a self-consistent set of input
parameters,
and to interpret the results correctly.
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?
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 :-)
Mark
3. in the top file it gives:
[ angles ]
;ai aj ak func th0(deg) Ka
1 2 3 1 0.95664E+02 0.40000E+02
2 3 4 1 0.91183E+02 0.40000E+02
3 4 5 1 0.89842E+02 0.40000E+02
4 5 6 1 0.91965E+02 0.40000E+02
5 6 7 1 0.90670E+02 0.40000E+02
6 7 8 1 0.91186E+02 0.40000E+02
7 8 9 1 0.92703E+02 0.40000E+02
8 9 10 1 0.91537E+02 0.40000E+02
9 10 11 1 0.91328E+02 0.40000E+02
10 11 12 1 0.92557E+02 0.40000E+02
11 12 13 1 0.93372E+02 0.40000E+02
12 13 14 1 0.94347E+02 0.40000E+02
13 14 15 1 0.99411E+02 0.40000E+02
14 15 16 1 0.98190E+02 0.40000E+02
......
[ dihedrals ]
;ai aj ak al func phi0(deg) Kd(kJ/mol) mult
1 2 3 4 1 0.24358E+03 0.10000E+01 1
1 2 3 4 1 0.73074E+03 0.50000E+00 3
2 3 4 5 1 0.22823E+03 0.10000E+01 1
2 3 4 5 1 0.68469E+03 0.50000E+00 3
3 4 5 6 1 0.23172E+03 0.10000E+01 1
3 4 5 6 1 0.69515E+03 0.50000E+00 3
4 5 6 7 1 0.22982E+03 0.10000E+01 1
4 5 6 7 1 0.68946E+03 0.50000E+00 3
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?
Has anyone used this webtool to do CG simulation and
explain what
is case?
Thank you all very much.
Ye
2011/6/22 Yang Ye <leafyo...@yahoo.com
<mailto:leafyo...@yahoo.com> <mailto:leafyo...@yahoo.com
<mailto:leafyo...@yahoo.com>>>
Hi,
The unit in output is in assumed to be for the
standard unit
input while the value is in reduced unit.
So you need to do your own calculation to figure out
what's
the reduced unit is.
Regards,
Yang Ye
On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang
<knightyang...@gmail.com
<mailto:knightyang...@gmail.com>
<mailto:knightyangpku@gmail.__com
<mailto:knightyang...@gmail.com>>> wrote:
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
<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
<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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==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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