[gmx-users]Question about reduced unit for coarse grain
Ye Yang
knightyangpku at gmail.com
Thu Jun 23 04:26:34 CEST 2011
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, it is developped by Dr. Onuchic's group
in UCSD.
Has anyone used this?
[ 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.Abraham at 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 <leafyoung at 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 <knightyangpku at 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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>>
>>
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>
>
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