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? 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)?
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 _______________________________________________ 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
