Re: [gmx-users] duplicated position restraint statements
That is way too much effort for not simply fixing the bug in the restraint generator, I hoped someone would just know off the top of their head ;) On Thu, Dec 20, 2018, 12:20 PM Justin Lemkul On Thu, Dec 20, 2018 at 2:08 PM Alex wrote: > > > Anyone? :) > > > > > Calculate a single-point energy on a given configuration with and without > duplicates. If the energy differs, you have your answer. > > -Justin > > > > > > On 12/16/2018 2:54 AM, Alex wrote: > > > Hi all, > > > > > > Quick question: in some of our models, the list of position restraints > > > as part of the permanent topology is created externally, based on the > > > atomic positions. Unfortunately, there is a slight bug in the > > > restraint generator and for a small portion of the restrained atoms > > > the statements are duplicated, i.e. there can be two identical > > > statements for something like four atoms out of ~200. Does grompp > > > interpret a duplicate as restraint with twice the force constants, is > > > it ignored? In other words, are duplicates additive? > > > > > > Thanks, > > > > > > Alex > > > > > -- > > 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. > > > > > -- > > == > > 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] duplicated position restraint statements
On Thu, Dec 20, 2018 at 2:08 PM Alex wrote: > Anyone? :) > > Calculate a single-point energy on a given configuration with and without duplicates. If the energy differs, you have your answer. -Justin > > On 12/16/2018 2:54 AM, Alex wrote: > > Hi all, > > > > Quick question: in some of our models, the list of position restraints > > as part of the permanent topology is created externally, based on the > > atomic positions. Unfortunately, there is a slight bug in the > > restraint generator and for a small portion of the restrained atoms > > the statements are duplicated, i.e. there can be two identical > > statements for something like four atoms out of ~200. Does grompp > > interpret a duplicate as restraint with twice the force constants, is > > it ignored? In other words, are duplicates additive? > > > > Thanks, > > > > Alex > > > -- > 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. > -- == 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.
Re: [gmx-users] duplicated position restraint statements
Anyone? :) On 12/16/2018 2:54 AM, Alex wrote: Hi all, Quick question: in some of our models, the list of position restraints as part of the permanent topology is created externally, based on the atomic positions. Unfortunately, there is a slight bug in the restraint generator and for a small portion of the restrained atoms the statements are duplicated, i.e. there can be two identical statements for something like four atoms out of ~200. Does grompp interpret a duplicate as restraint with twice the force constants, is it ignored? In other words, are duplicates additive? Thanks, Alex -- 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] duplicated position restraint statements
Hi all, Quick question: in some of our models, the list of position restraints as part of the permanent topology is created externally, based on the atomic positions. Unfortunately, there is a slight bug in the restraint generator and for a small portion of the restrained atoms the statements are duplicated, i.e. there can be two identical statements for something like four atoms out of ~200. Does grompp interpret a duplicate as restraint with twice the force constants, is it ignored? In other words, are duplicates additive? Thanks, Alex -- 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.
