Dear Mark Thank you for the kind response.
H with +0.418 charge and N with -0.845 charge is contributing towards coulomb 14 interaction. So what is the amount of interaction between one single H and N (3 bonds apart)? Kindly correct me if I am wrong. Here is my Gdm topology [ moleculetype ] ; name nrexcl GDM 3 [ atoms ] ; nr type resnr residu atom cgnr charge MASS 1 C 1 GND C1 1 1.027 13.019 2 NT 1 GND N2 2 -0.845 14.0067 3 H 1 GND H3 2 0.418 1.008 4 H 1 GND H4 2 0.418 1.008 5 NT 1 GND N5 3 -0.845 14.0067 6 H 1 GND H6 3 0.418 1.008 7 H 1 GND H7 3 0.418 1.008 8 NT 1 GND N8 4 -0.845 14.0067 9 H 1 GND H9 4 0.418 1.008 10 H 1 GND H10 4 0.418 1.008 [ bonds ] 1 2 2 0.1340 1.0500e+07 1 5 2 0.1340 1.0500e+07 1 8 2 0.1340 1.0500e+07 2 3 2 0.1000 1.8700e+07 2 4 2 0.1000 1.8700e+07 5 6 2 0.1000 1.8700e+07 5 7 2 0.1000 1.8700e+07 8 9 2 0.1000 1.8700e+07 8 10 2 0.1000 1.8700e+07 [ angles ] 1 2 3 2 120.00 390.00 1 2 4 2 120.00 390.00 1 5 6 2 120.00 390.00 1 5 7 2 120.00 390.00 1 8 9 2 120.00 390.00 1 8 10 2 120.00 390.00 3 2 4 2 120.00 445.00 6 5 7 2 120.00 445.00 9 8 10 2 120.00 445.00 2 1 5 2 120.00 670.00 5 1 8 2 120.00 670.00 8 1 2 2 120.00 670.00 [ pairs ] ; ai aj funct c0 c1 2 6 1 0.000000e+00 0.000000e+00 2 7 1 0.000000e+00 0.000000e+00 2 9 1 0.000000e+00 0.000000e+00 2 10 1 0.000000e+00 0.000000e+00 5 3 1 0.000000e+00 0.000000e+00 5 4 1 0.000000e+00 0.000000e+00 5 9 1 0.000000e+00 0.000000e+00 5 10 1 0.000000e+00 0.000000e+00 8 3 1 0.000000e+00 0.000000e+00 8 4 1 0.000000e+00 0.000000e+00 8 6 1 0.000000e+00 0.000000e+00 8 7 1 0.000000e+00 0.000000e+00 [ dihedrals ] ; ai aj ak al gromos type 2 1 5 6 1 180.000 33.5 2 2 1 5 7 1 180.000 33.5 2 2 1 8 9 1 180.000 33.5 2 2 1 8 10 1 180.000 33.5 2 5 1 2 3 1 180.000 33.5 2 5 1 2 4 1 180.000 33.5 2 5 1 8 9 1 180.000 33.5 2 5 1 8 10 1 180.000 33.5 2 8 1 2 3 1 180.000 33.5 2 8 1 2 4 1 180.000 33.5 2 Thank you Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University India > Hi, > > Presumably Gdm has atoms connected by three adjacent bonds that generally > have negative potential, and there's enough Gdm to make the total for the > system negative. It's generally a good idea to understand how the topology > you're using for Gdm works. > > Mark > > On Tue, Apr 10, 2018 at 2:23 PM <za...@tezu.ernet.in> wrote: > >> Dear Gromacs Users >> >> I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl) with >> gromos54a7 ff. Simulations have been performed for 100ns each at 298K, >> 350K and 450K. >> >> The Average Coulomb-14 Energies are as follows: >> >> ricin in water (298K) : 3.42E+04 (positive value) >> ricin in water (350K) : 3.41E+04 (positive value) >> ricin in water (450K) : 3.40E+04 (positive value) >> >> ricin + GdmCl (298K) :-3.16E+06 (negative value) >> ricin + GdmCl (350K) : -3.17E+06 (negative value) >> ricin + GdmCl (450K) : -3.17E+06 (negative value) >> >> Can anyone suggest me why there is a (10 to the power 10) fold >> difference >> of average Coulomb-14 energy of ricin in presence of water and ricin in >> presence of GdmCl? >> >> Thank You >> >> Regards >> >> Zaved * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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.