Re: [gmx-users] Purpose of repeated improper dihedrals
OK, I see. Thanks again! pt., 2 sie 2019 o 17:07 Justin Lemkul napisał(a): > > > On 8/2/19 8:59 AM, Dawid das wrote: > > Thank you for an asnwer. However, I still need to ask more. > > So, let's take this time the > > NR1 CPH1 CPH2 H > > NR1 CPH2 CPH1 H > > > > example. For such quartets, the improper dihedral parameters are defined > > for HSD residue. > > Now, the bonding is as follows in part of HSD: > >H > >| > > NR1 > >/\ > > CPH1CPH2 > > > > In my top file generated with pdb2gmx I can see the improper dihedral > > entries for both > > NR1 CPH1 CPH2 H > > NR1 CPH2 CPH1 H > > Also after dumping the tpr file I can see IDIHS entries for both > > arrangement of atoms for the same molecule. > > > > According to Gromacs manual, the entry for improper dihedral i j k l is > > understood as follows > > l > > | > > i > >/ \ > > j k > > > > So maybe I'm blind but I still don't really understand the purpose of > > changing the middle atom types > > if there is in fact only one way these four atoms are connected in HSD. > The > > only reason I see is to > > make it more rigid because I have "doubled" improper. > > Again, I would not call it a "doubled" parameter, because they are > clearly different in atom order. This usually implies a difference in > stereochemistry; in this case, I don't know the history of why the > impropers are assigned this way, but going back to the original CHARMM > topologies there are in fact two impropers assigned around ND1, CD2, and > CE1. The use of two terms with the same parameters but different > connectivities is probably due to having to avoid some kind of > asymmetry, though it seems unusual. Regardless, it is a faithful (and > correct) representation of the force field and we have tested it for > agreement between CHARMM and GROMACS. > > -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] Purpose of repeated improper dihedrals
On 8/2/19 8:59 AM, Dawid das wrote: Thank you for an asnwer. However, I still need to ask more. So, let's take this time the NR1 CPH1 CPH2 H NR1 CPH2 CPH1 H example. For such quartets, the improper dihedral parameters are defined for HSD residue. Now, the bonding is as follows in part of HSD: H | NR1 /\ CPH1CPH2 In my top file generated with pdb2gmx I can see the improper dihedral entries for both NR1 CPH1 CPH2 H NR1 CPH2 CPH1 H Also after dumping the tpr file I can see IDIHS entries for both arrangement of atoms for the same molecule. According to Gromacs manual, the entry for improper dihedral i j k l is understood as follows l | i / \ j k So maybe I'm blind but I still don't really understand the purpose of changing the middle atom types if there is in fact only one way these four atoms are connected in HSD. The only reason I see is to make it more rigid because I have "doubled" improper. Again, I would not call it a "doubled" parameter, because they are clearly different in atom order. This usually implies a difference in stereochemistry; in this case, I don't know the history of why the impropers are assigned this way, but going back to the original CHARMM topologies there are in fact two impropers assigned around ND1, CD2, and CE1. The use of two terms with the same parameters but different connectivities is probably due to having to avoid some kind of asymmetry, though it seems unusual. Regardless, it is a faithful (and correct) representation of the force field and we have tested it for agreement between CHARMM and GROMACS. -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.
Re: [gmx-users] Purpose of repeated improper dihedrals
Thank you for an asnwer. However, I still need to ask more. So, let's take this time the NR1 CPH1 CPH2 H NR1 CPH2 CPH1 H example. For such quartets, the improper dihedral parameters are defined for HSD residue. Now, the bonding is as follows in part of HSD: H | NR1 /\ CPH1CPH2 In my top file generated with pdb2gmx I can see the improper dihedral entries for both NR1 CPH1 CPH2 H NR1 CPH2 CPH1 H Also after dumping the tpr file I can see IDIHS entries for both arrangement of atoms for the same molecule. According to Gromacs manual, the entry for improper dihedral i j k l is understood as follows l | i / \ j k So maybe I'm blind but I still don't really understand the purpose of changing the middle atom types if there is in fact only one way these four atoms are connected in HSD. The only reason I see is to make it more rigid because I have "doubled" improper. Best regards, Dawid Grabarek pt., 2 sie 2019 o 13:40 Justin Lemkul napisał(a): > > > On 8/2/19 2:38 AM, Dawid das wrote: > > Dear All, > > > > Why some of the improper parameters in CHARMM27 FF are repeated with > > the middle atom types in a different order as in, e.g. > > > > HR1 NR1 NR2 CPH22 0. 4.184 > > HR1 NR2 NR1 CPH22 0. 4.184 > > These aren't repeated parameters. They are different parameters > corresponding to different connectivity. > > -Justin > > > while some are not, e.g. > > HR3 CPH1NR3 CPH12 0. 8.368 > > > > Best regards, > > Dawid Grabarek > > -- > == > > 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] Purpose of repeated improper dihedrals
On 8/2/19 2:38 AM, Dawid das wrote: Dear All, Why some of the improper parameters in CHARMM27 FF are repeated with the middle atom types in a different order as in, e.g. HR1 NR1 NR2 CPH22 0. 4.184 HR1 NR2 NR1 CPH22 0. 4.184 These aren't repeated parameters. They are different parameters corresponding to different connectivity. -Justin while some are not, e.g. HR3 CPH1NR3 CPH12 0. 8.368 Best regards, Dawid Grabarek -- == 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] Purpose of repeated improper dihedrals
Dear All, Why some of the improper parameters in CHARMM27 FF are repeated with the middle atom types in a different order as in, e.g. HR1 NR1 NR2 CPH22 0. 4.184 HR1 NR2 NR1 CPH22 0. 4.184 while some are not, e.g. HR3 CPH1NR3 CPH12 0. 8.368 Best regards, Dawid Grabarek -- 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.
