[gmx-users] Wall potential

Hi Gomacians, I want to use implicit wall. I set the mdp parameters as follows. nwall= 2 wall_type= 9-3 wall_r_linpot= 1 wall_atomtype= Au Au wall_density = 58.01 58.01 wall_ewald_zfac = 3 Also set LJ p

Re: [gmx-users] SWM4-NDP WATER MODEL AND IONS

On Fri, Feb 10, 2012 at 4:11 PM, David van der Spoel wrote: > > Op 10 feb 2012 om 22:55 heeft Abhijeet Joshi het > volgende geschreven: > > Hi , > I am also working on similar systems. Can you tell me where and > what LJ parameters you specified for halides > >

Re: [gmx-users] SWM4-NDP WATER MODEL AND IONS

2 > 2 1 > [ moleculetype ] > ; molname nrexcl > CS 1 > [ atoms ] > ; idat type res nr residu name at name cg nr charge > 1 CSc 1 CScCSc 13.665877 > 2 CSs 1 CSsCSs

Re: [gmx-users] Polarizable halide (Iodide)

Oh ohk, I have been running in parallel Thanks David, On Tue, Mar 1, 2011 at 3:12 PM, David van der Spoel wrote: > On 2011-03-01 22.06, Abhijeet Joshi wrote: > >> Hi all, >> >>I am trying implement polarizable model for halides >> suggested by R

[gmx-users] Polarizable halide (Iodide)

Hi all, I am trying implement polarizable model for halides suggested by Roux group. I am not able to equilibrate such system. System: Sodium Iodide in water I am using following topology file for iodide. Anybody has any clue what might be happening? Question 2: I am having trouble f

[gmx-users] Surface pressure for lipid bilayer.

Hi, As correctly pointed out by Mark, I am restating my concern in this topic. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I won't

Re: [gmx-users] question about periodic boundary conditions

Hi, I am new to the list. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I won't get a meaningful value because of large fluctuations.