Justin, 1) I've already tried to examine this graphs but have not understood the meaning of the Ro value.
E.g I have known distance restrains for the pair of residue wich are 1<r< 2 for instance. As I understood the R1=1 and R2=2 but what about R0 ?As I've understood this value might be slightly less than R1 ( e.g 0.9). Does this correct and how I could specify R0 more accuracy? 2) Besides I want to know if there are possible way to gradyally decrease force constants during MD run? E.g I want to dicrease this value each 100ps on the desired value. Is there any way to defind this step value in the MDP file or should I re-run mu simulation X times started from the previous short run with bigger forses applied? James 13 марта 2012 г. 17:19 пользователь Justin A. Lemkul <jalem...@vt.edu>написал: > > > James Starlight wrote: > >> Mark, Justin, >> >> Thanks for advises. Indeed I think that simple text editor would be >> better sollution in my casw because of small number of restraints. >> >> I just have a question about definition of the Distances >> >> This is the default of the restraints between atom 10 and 16. >> >> [ distance_restraints ] >> ; ai aj type index type' low up1 up2 fac >> 10 16 1 0 1 0.0 0.3 0.4 1.0 >> >> >> >> I'd like to restrict distance between both of that atoms 7.96 < >> r(Ca-Ca)< 8.41 >> >> I've found that the up1 is the 7.96 and up2 is the 8.41 but how I could >> specify 'low' in the above table ? Should I obtain value for the initial >> Ca-Ca distance between my residues from the initial structure? How I could >> do it? >> >> > See Figure 4.13 and equations 4.79 in the manual. r0 = low, r1 = up1, and > r2 = up2. > > > -Justin > > -- > ==============================**========== > > 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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