Re: [gmx-users] Ewald summation in 2 dimensions with correction

2017-11-12 Thread David van der Spoel
On 11/11/17 16:44, Dan Gil wrote: Hi, Just wanted to see if anyone had any thoughts... For more information, if I use: wall-ewald-zfac = 3 E-z= 1 5 0 The electric field from ionic liquid has a magnitude of 7.5 V/nm in the opposite direction to the applied electric field.

Re: [gmx-users] mobile ligand with intermolecular interactions

2017-11-12 Thread Ahmet Yildirim
Hi, Let me take that in reverse order: > > Note that choosing appropriate atoms to apply restraints is not a trivial > matter, and results can vary depending on the choices made. > I know. I doubt there's a bug. I tested this feature a lot myself and have used it. > How different are the

[gmx-users] Najam

2017-11-12 Thread Najamuddin Memon
I am working on MD simulation while using Gromacs. I want to simulate acetylated protein with DNA. Which type of force field I have to use that encompass both DNA and acetylated histones parameters. Regards Najam QAU, Pakistan. Sent from Mail for Windows 10 -- Gromacs Users mailing list

Re: [gmx-users] Gromacs simulation with PEG

2017-11-12 Thread Amali Guruge
Dear Gromacs Users, Thank you very much. On Mon, Nov 13, 2017 at 9:56 AM, Justin Lemkul wrote: > > > On 11/12/17 5:51 PM, Amali Guruge wrote: > >> Dear Gromacs users, >> >> I tried to simulate a system which contains PEG and water. According to >> the >> phase diagram of PEG,

Re: [gmx-users] Gromacs simulation with PEG

2017-11-12 Thread Justin Lemkul
On 11/12/17 5:51 PM, Amali Guruge wrote: Dear Gromacs users, I tried to simulate a system which contains PEG and water. According to the phase diagram of PEG, it should form micells after the simulation. However, after the simulation PEG doesn't form micells. What could be the reason for

Re: [gmx-users] mobile ligand with intermolecular interactions

2017-11-12 Thread Justin Lemkul
On 11/10/17 11:59 PM, Ahmet Yildirim wrote: Hi, Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is used at end of the complex topology file. This is a bug? I doubt there's a bug. I tested this

Re: [gmx-users] Gromacs simulation with PEG

2017-11-12 Thread Dallas Warren
You used the incorrect forcefield. We have found that GROMOS53a6 and associated forcefields reproduce poorly the interactions between PEG and water. We have made improvements on that, and will be publishing something soon. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics

[gmx-users] Gromacs simulation with PEG

2017-11-12 Thread Amali Guruge
Dear Gromacs users, I tried to simulate a system which contains PEG and water. According to the phase diagram of PEG, it should form micells after the simulation. However, after the simulation PEG doesn't form micells. What could be the reason for this. Can anyone help me. Thank you. -- Gromacs