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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