Re: [gmx-users] Problem force constant bond stretc.
Thanks a lot. Best regards, Paolo Il giorno gio 16 apr 2020 alle ore 07:57 David van der Spoel < sp...@xray.bmc.uu.se> ha scritto: > Den 2020-04-15 kl. 23:48, skrev Paolo Costa: > > Dear Gromacs users, > > > > I have a problem regarding force constant for bond stretching. By > employing > > VFFDT software, I got C-C bond stretching force constant (for Benzene, > > B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to > > 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of > > Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It > > seems that the value I got from VFFDT is somehow half than the one > reported > > in Amber force field. > > Can somebody help me to figure out such issue? > > > > Thanks a lot in advance for your help. > > > Vbond = (k/2) (r - r0)^2 > > Some methods do not use the division by two, so it can be a matter of > definition. > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] Problem force constant bond stretc.
Den 2020-04-15 kl. 23:48, skrev Paolo Costa: Dear Gromacs users, I have a problem regarding force constant for bond stretching. By employing VFFDT software, I got C-C bond stretching force constant (for Benzene, B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It seems that the value I got from VFFDT is somehow half than the one reported in Amber force field. Can somebody help me to figure out such issue? Thanks a lot in advance for your help. Vbond = (k/2) (r - r0)^2 Some methods do not use the division by two, so it can be a matter of definition. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.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.
[gmx-users] Problem force constant bond stretc.
Dear Gromacs users, I have a problem regarding force constant for bond stretching. By employing VFFDT software, I got C-C bond stretching force constant (for Benzene, B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It seems that the value I got from VFFDT is somehow half than the one reported in Amber force field. Can somebody help me to figure out such issue? Thanks a lot in advance for your help. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.