Re: [gmx-users] Fwd: I have a symmetric simulation box,

2012-10-18 Thread Justin Lemkul
On 10/18/12 6:45 AM, Ali Alizadeh wrote: Dear Justin Please check my commands, Are these correct, step by step? If these are correct then i will start my simulation with longer time, I really don't understand why you're invoking pdb2gmx three times. You should only ever need to produce

Re: [gmx-users] Fwd: I have a symmetric simulation box,

2012-10-18 Thread Justin Lemkul
On 10/18/12 6:15 AM, Erik Marklund wrote: 18 okt 2012 kl. 12.08 skrev Ali Alizadeh: Dear All users 1- I have a symmetric simulation box but i can not produce a symmetric number density result (number density vs. z direction(nm)) My simulation box is orthorhombic. My boundary condition is p

Re: [gmx-users] Fwd: I have a symmetric simulation box,

2012-10-18 Thread Erik Marklund
18 okt 2012 kl. 12.08 skrev Ali Alizadeh: > Dear All users > > 1- I have a symmetric simulation box but i can not produce a symmetric > number density result (number density vs. z direction(nm)) > > My simulation box is orthorhombic. My boundary condition is pbc but i > don't perform any comman