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.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> > >> 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>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@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-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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