[gmx-users]Question about reduced unit for coarse grain
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 23 04:32:57 CEST 2011
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, 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.Abraham at anu.edu.au
> <mailto: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 <mailto: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 <mailto: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
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list