[gmx-users] question about periodic boundary conditions

Hi, Is there a way to quantitatively determine, from a trajectory file, whether a molecule is interacting with a copy of itself in the adjacent box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure file and viewed the periodic images

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

rainy...@yahoo.com wrote: Hi, Is there a way to quantitatively determine, from a trajectory file, whether a molecule is interacting with a copy of itself in the adjacent box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure

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

rainy...@yahoo.com wrote: Hi Justin, Thanks for getting back to me. I executed the following command using g_mindist: $gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n index.ndx -od mindist.xvg ..and got the output (see below). It shows that the minimal distance to

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

Justin, I have a single solute. But I understand what you're saying about the cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force field), so therefore, the snapshots corresponding to a minimum periodic distance of 1.2 nm would agree with the overlap witnessed in VMD? Thanks

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

rainy...@yahoo.com wrote: Justin, I have a single solute. But I understand what you're saying about the cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force field), so therefore, the snapshots corresponding to a minimum periodic distance of 1.2 nm would agree with the

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.

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

On 21/10/2010 10:45 AM, Abhijeet Joshi wrote: 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