Re: [gmx-users] minimum distance between the protein and its mirror image

On 8/29/16 9:20 PM, OuyangYanhua wrote: The minimum protein-image distance is less than the value 2.0nm, such as t around 1.6nm above. Does it mean my simulation is failed in the box size set? Please read the first sentence of my previous reply. -Justin 在 2016年8月29日，下午8:58，Justin Lemkul

Re: [gmx-users] minimum distance between the protein and its mirror image

The minimum protein-image distance is less than the value 2.0nm, such as t around 1.6nm above. Does it mean my simulation is failed in the box size set? > 在 2016年8月29日，下午8:58，Justin Lemkul 写道： > > > > On 8/29/16 5:02 AM, YanhuaOuyang wrote: >> Hi, >> I am running a REMD of

Re: [gmx-users] minimum distance between the protein and its mirror image

On 8/29/16 5:02 AM, YanhuaOuyang wrote: Hi, I am running a REMD of a disordered protein, I visualized the trajectory in VMD and I found that the protein is very close to the box edge. Then I use "gmx mindist " to check if a protein has seen its periodic image during simulation. When

[gmx-users] minimum distance between the protein and its mirror image

Hi, I am running a REMD of a disordered protein, I visualized the trajectory in VMD and I found that the protein is very close to the box edge. Then I use "gmx mindist " to check if a protein has seen its periodic image during simulation. When I used the command "gmx mindist -f