Hi, It's actually a bit more nuanced and the use of these idioms is not really backed by a semantic distinction: In Gromacs, a constraint fixes some property to a value, whereas a restraint penalizes deviation of a property from a certain value.
Cheers, Tsjerk On Wed, Sep 30, 2009 at 2:03 AM, Justin A. Lemkul <[email protected]> wrote: > > > Payman Pirzadeh wrote: >> >> Hi, I read the wiki and manual on constraint and restraints, and I am >> still a >> bit confused. But, my question is, should I remove the restraints after >> equilibration in production phase? > > A restraint fixes the position of an atom, or the value of an angle, > dihedral, etc. So, if you'd like your molecule of interest to actually do > something during data collection, yes, remove restraints :) > >> What about constraints? How should I know my system really needs either of >> them (is there a general rule or protocol to follow)? If I apply them >> incorrectly, how will them affect my results (in my case protein)? >> > > A constraint fixes a bond length. If you don't use constraints, you must > use a very small dt, like 0.5 fs. Use of constraints allows you to use a dt > of 1-2 fs (or more if using virtual sites). The LINCS papers (cited in the > manual) describe the background of these methods. If you apply constraints > incorrectly (i.e., by not using them and then implementing dt of 2 fs), your > system will either rapidly collapse, or your total energy will not be > conserved. > > -Justin > >> Payman >> >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] >> On Behalf Of Justin A. Lemkul >> Sent: September 17, 2009 5:38 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] merging simulation boxes >> >> >> >> Paymon Pirzadeh wrote: >>> >>> I have a box of crystal (from another simulation) and a box of solvated >>> protein. Now I want to put the protein close to my crystal. >>> >> >> Use editconf to define a box for your new system, use -center on each >> component as appropriate, and cat the two .gro files together (removing >> the duplicate >> box info, etc that will be placed in the middle of the new file). >> >> -Justin >> >>> Payman >>> >>> >>> >>> >>> On Fri, 2009-09-18 at 09:04 +1000, Mark Abraham wrote: >>>> >>>> Paymon Pirzadeh wrote: >>>>> >>>>> Hello, >>>>> Are there any links on how we can merge two simulation boxes to make a >>>>> single configuration? What technicalities should be considered? >>>> >>>> Define "merge". There's a whole pile of issues depending what you mean. >>>> >>>> Why can't you build initial coordinates up from scratch, rather than >>>> "merge" some pre-existing sets? >>>> >>>> Mark >>>> _______________________________________________ >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >> >> posting! >>>> >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to [email protected]. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
