Re: [gmx-users] use of DPOSRES without pdb2gmx
Justin, Thanks, Bartimaeus -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Thursday, January 17, 2019 2:44 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] use of DPOSRES without pdb2gmx On 1/17/19 3:33 PM, pbusc...@q.com wrote: > Dear Users, > > Suppose you do not use pdb2gmx and therefore do not use the -I > option for all constraints. Suppose further you do not generate a > restraint file for the non-protein molecules in the model. > > Then what effect, if any, does setting constraints = all-bonds or > h-bonds have ? Constraints and restraints are totally different. If you tell mdrun to constrain bonds, it will do precisely what you tell it. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] use of DPOSRES without pdb2gmx
On 1/17/19 3:33 PM, pbusc...@q.com wrote: Dear Users, Suppose you do not use pdb2gmx and therefore do not use the -I option for all constraints. Suppose further you do not generate a restraint file for the non-protein molecules in the model. Then what effect, if any, does setting constraints = all-bonds or h-bonds have ? Constraints and restraints are totally different. If you tell mdrun to constrain bonds, it will do precisely what you tell it. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] use of DPOSRES without pdb2gmx
Dear Users, Suppose you do not use pdb2gmx and therefore do not use the -I option for all constraints. Suppose further you do not generate a restraint file for the non-protein molecules in the model. Then what effect, if any, does setting constraints = all-bonds or h-bonds have ? Thanks Paul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
