Re: [gmx-users] comm-grps problem gromacs 4.0.4

Oliver Grant wrote: Thanks for the help, With center of mass removal option I thought my sugar would stay in the center of the box. It does in the first simulation I ran however what I mean by diffuse is that it leaves the box on one side and enters from the other. There is nothing physical

Re: [gmx-users] comm-grps problem gromacs 4.0.4

Thanks for the help, With center of mass removal option I thought my sugar would stay in the center of the box. It does in the first simulation I ran however what I mean by diffuse is that it leaves the box on one side and enters from the other. There is nothing physically wrong with this but I'd

Re: [gmx-users] comm-grps problem gromacs 4.0.4

Oliver Grant wrote: Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = and comm-grps = carb and what is below. Why wouldn't your trisaccharide diffuse around? The only approp

[gmx-users] comm-grps problem gromacs 4.0.4

Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = and comm-grps = carb and what is below. carb is the name I use in my top file and index file. For the index I specify the groups in