Thank you very much! I will check with them carefully. Ye
2011/6/23 Justin A. Lemkul <jalem...@vt.edu> > > > Ye Yang wrote: > >> Just no reply from them for some time... >> > > Well, that's unfortunate. I'd hazard a guess that all the units are > reduced, but that's just a hunch. Theoretically, all your input and output > should be in reduced units. My hunch is based on the fact that everything > shown (in terms of force constants) is a nice, round number (5, 10, 400) > which seems odd for standard values (see any ffbonded.itp for "normal" > values). It looks like everything is relative to the reduced units, but to > be sure you'd really have to get a response from those who developed the web > service you're trying to use, if this information is not otherwise > documented somewhere (FAQ's, publication, etc). > > -Justin > > Thank you anyway. >> >> Ye >> 2011/6/22 Justin A. Lemkul <jalem...@vt.edu <mailto: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> >> >> <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>> >> <mailto: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> <mailto: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>> >> <mailto:knightyangpku@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> >> >> <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> >> >> <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> >> <mailto: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> >> >> <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> >> >> <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. 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Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <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 >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <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. 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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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