Re: [gmx-users] seeming paradox with gmx wham

You actually pointed this symmetry situation out when I was calculating something that's already been submitted, so the gratitude is all mine. Hopefully, it doesn't produce much of a difference in that particular case, but I really should have listened. The path to correcting possible artifacts is

Re: [gmx-users] seeming paradox with gmx wham

On 3/12/18 6:59 PM, Alex wrote: Great, thanks. I believe this necessitates an acknowledgment. You go by J. A. Lemkul in your papers, correct? That would work. Much obliged :) -Justin On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul wrote: r On 3/12/18 6:54 PM, Alex

Re: [gmx-users] seeming paradox with gmx wham

Great, thanks. I believe this necessitates an acknowledgment. You go by J. A. Lemkul in your papers, correct? On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul wrote: > r > > On 3/12/18 6:54 PM, Alex wrote: > >> Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point,

Re: [gmx-users] seeming paradox with gmx wham

r On 3/12/18 6:54 PM, Alex wrote: Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's still a small system. My sampling pull code is below, I only modified the bare minimum to work with the new pull code syntax and to enable spherical slices (radius varying from near-zero

Re: [gmx-users] seeming paradox with gmx wham

Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's still a small system. My sampling pull code is below, I only modified the bare minimum to work with the new pull code syntax and to enable spherical slices (radius varying from near-zero to 1.5 nm): pull =

Re: [gmx-users] seeming paradox with gmx wham

On 3/12/18 3:42 PM, Alex wrote: I actually understood your tutorial perfectly well. What I didn't expect is such a significant dependence on direction (assuming spherical symmetry clears the situation). I also had to use direction-periodic instead of distance in your tutorial, because the

Re: [gmx-users] seeming paradox with gmx wham

Sorry, i meant 4 nm tall, not wide. On 3/12/2018 1:42 PM, Alex wrote: I actually understood your tutorial perfectly well. What I didn't expect is such a significant dependence on direction (assuming spherical symmetry clears the situation). I also had to use direction-periodic instead of

Re: [gmx-users] seeming paradox with gmx wham

I actually understood your tutorial perfectly well. What I didn't expect is such a significant dependence on direction (assuming spherical symmetry clears the situation). I also had to use direction-periodic instead of distance in your tutorial, because the box is 4 nm wide and grompp is

Re: [gmx-users] seeming paradox with gmx wham

On 3/12/18 3:28 PM, Alex wrote: Thanks! Just to make sure I'm doing this right this time. By merely changing the dim directive with everything else following your tutorial, I would be probing the spherical domain around the pore with a bunch of different radius values? Because this is

Re: [gmx-users] seeming paradox with gmx wham

Thanks! Just to make sure I'm doing this right this time. By merely changing the dim directive with everything else following your tutorial, I would be probing the spherical domain around the pore with a bunch of different radius values? Because this is exactly what I want. Thanks, Alex

Re: [gmx-users] seeming paradox with gmx wham

On 3/11/18 8:05 PM, Alex wrote: Just to add to my question... The pull code for the umbrella sampling from each of the N configs, as used in Justin's tutorial, is pull_coord1_type    = umbrella pull_coord1_geometry    = distance ... pull_coord1_dim = N N Y So, in each of the

Re: [gmx-users] seeming paradox with gmx wham

Just to add to my question... The pull code for the umbrella sampling from each of the N configs, as used in Justin's tutorial, is pull_coord1_type= umbrella pull_coord1_geometry= distance ... pull_coord1_dim = N N Y So, in each of the generated pullf and pullx files we