Re: [gmx-users] Neutralizing

Thank you Justin for your help. On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul wrote: On 3/9/16 1:42 AM, mohammad r wrote: > Thank you Parham and Justin, Excuse me I have another question, in simulation > of a water-peptide system, is it necessary to use QM/MM

Re: [gmx-users] Neutralizing

On 3/9/16 1:42 AM, mohammad r wrote: Thank you Parham and Justin, Excuse me I have another question, in simulation of a water-peptide system, is it necessary to use QM/MM simulation during the entire process? Because I didn't see it in the tutorials. By the way I generated the pdb file by

Re: [gmx-users] Neutralizing

Thank you Parham and Justin, Excuse me I have another question, in simulation of a water-peptide system, is it necessary to use QM/MM simulation during the entire process? Because I didn't see it in the tutorials. By the way I generated the pdb file by using charmm-gui then import it in amber

Re: [gmx-users] Neutralizing

On 3/8/16 3:59 AM, mohammad r wrote: Thank you Parham You mean that it is not necessary to do QM/MM simulation? The trivial task of adding ions to neutralize the net charge on the system certainly does not require anything like QM/MM. -Justin On Tuesday, March 8, 2016 11:13 AM,

Re: [gmx-users] Neutralizing

Thank you Parham You mean that it is not necessary to do QM/MM simulation? On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical Science) wrote: Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral

Re: [gmx-users] Neutralizing

Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral In this case, you don't need ​the number of ions​. Kind Regards Parham J. K. ** *​​* *==* *​==​* *=* ​PhD candidate - Lecturer in drug discovery Faculty of Medicine and Health

[gmx-users] Neutralizing

Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at