[ 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>>
__
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>>
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>> 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),
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), 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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