Just no reply from them for some time... Thank you anyway. Ye 2011/6/22 Justin A. Lemkul <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 <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:knightyangpku@gmail.**com<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 >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive at >>> >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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-requ...@gromacs.org >>> >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >. >>> >>> Can't post? Read http://www.gromacs.org/** >>> Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive at >>> >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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-requ...@gromacs.org >>> >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >. >>> >>> Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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