[gmx-users] Adding proton using genion to study proton transfer reaction

Dear GMxers, I want to simulate the proton transfer reaction in bulk water using gromacs.I am not aware how to add proton using genion.Is it possible to add excess protons like other ions.I could not find proton in ions.itp. If anybody can guide me about the same. Thanks DeepaK Ojha School

[gmx-users] Genion command not working

file: ../../../../src/tools/gmx_genion.c, line: 85 Fatal error: No more replaceable solvent! --- How should I add ions in the system.I have tried doing it but could not get it please if someone may point my error. -- DeepaK Ojha School

[gmx-users] simulation of liquid water interface in electric field

is equilibrated and even during production what should be the parameter of check to see the system does not moves away from the minima. I have conceptual doubt hope you all will entertain it. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live

[gmx-users] Instantaneous dipole moment of water molecule

been strongly demotivated in previous discussions.Please help me in this regard. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] segmentation fault with mdrun

180.0 41840001.2 ;N1 N2 N3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Topology file for simulation of inorganic compounds

Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes

[gmx-users] D20 simulation/Topology file and force field

Dear All I want to perform simulation of pure D20 in gromacs. I found that there is no inbuilt model of heavy water in gromacs.How should I generate topology file,itp file and which force field should I use. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live

[gmx-users] Calculation of instantaneous dipole moment through Gromacs

of using polarizable water model with flexible charges in GROMACS. -- DeepaK Ojha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists