Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

2017-11-14 Thread Suman Das
Thank you Prof. David for your reply and sorry for the late response. So, now, do I have to use the original traj.xtc or still I need to do least square fitting w.r.t the C-alpha atom and removal of translation/rotational motion? Thanks, Suman On 31/10/17 20:56, Suman Das wrote: > > Dear Gromacs

Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

2017-11-09 Thread David van der Spoel
On 08/11/17 20:11, Suman Das wrote: Thank you Prof. David for your reply and sorry for the late response. So, now do I have to use the original traj.xtc or still I need to do least square fitting w.r.t the C-alpha atom? Thanks, Suman Neither. Please read my instructions carefully, you need to b

Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

2017-11-08 Thread Suman Das
Thank you Prof. David for your reply and sorry for the late response. So, now do I have to use the original traj.xtc or still I need to do least square fitting w.r.t the C-alpha atom? Thanks, Suman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Maili

Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

2017-10-31 Thread David van der Spoel
On 31/10/17 20:56, Suman Das wrote: Dear Gromacs Users, I am trying to calculate static dielectric constant of Lysozymes using gromacs version 4.6.7. I tried to follow the protocol used earlier by van Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014). I used PME for the electrostatic interaction.

[gmx-users] Problem in calculating static dielectric constant of Lysozymes

2017-10-31 Thread Suman Das
Dear Gromacs Users, I am trying to calculate static dielectric constant of Lysozymes using gromacs version 4.6.7. I tried to follow the protocol used earlier by van Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014). I used PME for the electrostatic interaction. First, I converted the trajectory of p