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 clear. :) Alex On Mon, Mar 12, 2018 at 5:03 PM, Justin Lemkul wrote: > > > 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 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 to 1.5 nm): pull = yes pull-coord1-type = umbrella pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= CL pull_group2_name= CNT pull_coord1_geometry= distance pull_coord1_groups = 1 2 pull_dim= Y Y Y pull_coord1_rate= 0.0 pull_coord1_k = 1000 pull_start = yes CNT is the colloquial name for our membrane. I'm trying to be extra-careful this time, so I will really appreciate if you see anything else that looks wrong. Another quick question: it is my understanding that the value of k will control the histogram width. Is 1000 a reasonable choice overall? No way to know. It depends on the window spacing and the forces acting >>> in >>> the system. I don't know that anyone has come up with a way to actually >>> know what's "right" for umbrella sampling other than empirical >>> assignment. >>> >>> Everything else looks reasonable to me. >>> >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> == >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 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 to 1.5 nm): pull = yes pull-coord1-type = umbrella pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= CL pull_group2_name= CNT pull_coord1_geometry= distance pull_coord1_groups = 1 2 pull_dim= Y Y Y pull_coord1_rate= 0.0 pull_coord1_k = 1000 pull_start = yes CNT is the colloquial name for our membrane. I'm trying to be extra-careful this time, so I will really appreciate if you see anything else that looks wrong. Another quick question: it is my understanding that the value of k will control the histogram width. Is 1000 a reasonable choice overall? No way to know. It depends on the window spacing and the forces acting in the system. I don't know that anyone has come up with a way to actually know what's "right" for umbrella sampling other than empirical assignment. Everything else looks reasonable to me. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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, 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 = yes >> pull-coord1-type = umbrella >> pull_ngroups= 2 >> pull_ncoords= 1 >> pull_group1_name= CL >> pull_group2_name= CNT >> pull_coord1_geometry= distance >> pull_coord1_groups = 1 2 >> pull_dim= Y Y Y >> pull_coord1_rate= 0.0 >> pull_coord1_k = 1000 >> pull_start = yes >> >> CNT is the colloquial name for our membrane. I'm trying to be >> extra-careful >> this time, so I will really appreciate if you see anything else that looks >> wrong. Another quick question: it is my understanding that the value of k >> will control the histogram width. Is 1000 a reasonable choice overall? >> > > No way to know. It depends on the window spacing and the forces acting in > the system. I don't know that anyone has come up with a way to actually > know what's "right" for umbrella sampling other than empirical assignment. > > Everything else looks reasonable to me. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 to 1.5 nm): pull = yes pull-coord1-type = umbrella pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= CL pull_group2_name= CNT pull_coord1_geometry= distance pull_coord1_groups = 1 2 pull_dim= Y Y Y pull_coord1_rate= 0.0 pull_coord1_k = 1000 pull_start = yes CNT is the colloquial name for our membrane. I'm trying to be extra-careful this time, so I will really appreciate if you see anything else that looks wrong. Another quick question: it is my understanding that the value of k will control the histogram width. Is 1000 a reasonable choice overall? No way to know. It depends on the window spacing and the forces acting in the system. I don't know that anyone has come up with a way to actually know what's "right" for umbrella sampling other than empirical assignment. Everything else looks reasonable to me. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 = yes pull-coord1-type = umbrella pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= CL pull_group2_name= CNT pull_coord1_geometry= distance pull_coord1_groups = 1 2 pull_dim= Y Y Y pull_coord1_rate= 0.0 pull_coord1_k = 1000 pull_start = yes CNT is the colloquial name for our membrane. I'm trying to be extra-careful this time, so I will really appreciate if you see anything else that looks wrong. Another quick question: it is my understanding that the value of k will control the histogram width. Is 1000 a reasonable choice overall? Thank you, Alex On Mon, Mar 12, 2018 at 4:07 PM, Justin Lemkul wrote: > > > 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 box is 4 nm wide and grompp is screaming about >> distance exceeding half-box size. I used 5.0.3 before and it was fine with >> the 'distance' directive. I think 'direction-periodic' is also wrong for >> spherical symmetry. So, stick with distance and increase box size? >> >> That's the easiest thing to do, yes, as long as the simulation is still > reasonably efficient. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 box is 4 nm wide and grompp is screaming about distance exceeding half-box size. I used 5.0.3 before and it was fine with the 'distance' directive. I think 'direction-periodic' is also wrong for spherical symmetry. So, stick with distance and increase box size? That's the easiest thing to do, yes, as long as the simulation is still reasonably efficient. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 distance in your tutorial, because the box is 4 nm wide and grompp is screaming about distance exceeding half-box size. I used 5.0.3 before and it was fine with the 'distance' directive. I think 'direction-periodic' is also wrong for spherical symmetry. So, stick with distance and increase box size? Thanks, Alex On 3/12/2018 1:35 PM, Justin Lemkul wrote: 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 exactly what I want. Yes, you're applying a 1-D bias when you actually want a 3-D bias. People often misuse the tutorial .mdp files, though I will have a new version of the tutorial out this summer (along with a paper) that should clear all this up. -Justin Thanks, Alex On 3/12/2018 8:43 AM, Justin Lemkul wrote: 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 generated pullf and pullx files we sample a flat slice at a given Z, and the reported forces and displacements are along Z. What appears to be the reaction coordinate in our case is the radius from the pore mouth, and one has to sample a set of hemispheres from a series of radius values. Is this at all a possibility? Yes, but not by following the tutorial. You'd need to use pull_coord1_dim = Y Y Y to restrict the ions to a given radius around the pore itself. As it is, you're probably underestimating entropic contributions to the free energy. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 screaming about distance exceeding half-box size. I used 5.0.3 before and it was fine with the 'distance' directive. I think 'direction-periodic' is also wrong for spherical symmetry. So, stick with distance and increase box size? Thanks, Alex On 3/12/2018 1:35 PM, Justin Lemkul wrote: 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 exactly what I want. Yes, you're applying a 1-D bias when you actually want a 3-D bias. People often misuse the tutorial .mdp files, though I will have a new version of the tutorial out this summer (along with a paper) that should clear all this up. -Justin Thanks, Alex On 3/12/2018 8:43 AM, Justin Lemkul wrote: 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 generated pullf and pullx files we sample a flat slice at a given Z, and the reported forces and displacements are along Z. What appears to be the reaction coordinate in our case is the radius from the pore mouth, and one has to sample a set of hemispheres from a series of radius values. Is this at all a possibility? Yes, but not by following the tutorial. You'd need to use pull_coord1_dim = Y Y Y to restrict the ions to a given radius around the pore itself. As it is, you're probably underestimating entropic contributions to the free energy. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 exactly what I want. Yes, you're applying a 1-D bias when you actually want a 3-D bias. People often misuse the tutorial .mdp files, though I will have a new version of the tutorial out this summer (along with a paper) that should clear all this up. -Justin Thanks, Alex On 3/12/2018 8:43 AM, Justin Lemkul wrote: 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 generated pullf and pullx files we sample a flat slice at a given Z, and the reported forces and displacements are along Z. What appears to be the reaction coordinate in our case is the radius from the pore mouth, and one has to sample a set of hemispheres from a series of radius values. Is this at all a possibility? Yes, but not by following the tutorial. You'd need to use pull_coord1_dim = Y Y Y to restrict the ions to a given radius around the pore itself. As it is, you're probably underestimating entropic contributions to the free energy. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 On 3/12/2018 8:43 AM, Justin Lemkul wrote: 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 generated pullf and pullx files we sample a flat slice at a given Z, and the reported forces and displacements are along Z. What appears to be the reaction coordinate in our case is the radius from the pore mouth, and one has to sample a set of hemispheres from a series of radius values. Is this at all a possibility? Yes, but not by following the tutorial. You'd need to use pull_coord1_dim = Y Y Y to restrict the ions to a given radius around the pore itself. As it is, you're probably underestimating entropic contributions to the free energy. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 generated pullf and pullx files we sample a flat slice at a given Z, and the reported forces and displacements are along Z. What appears to be the reaction coordinate in our case is the radius from the pore mouth, and one has to sample a set of hemispheres from a series of radius values. Is this at all a possibility? Yes, but not by following the tutorial. You'd need to use pull_coord1_dim = Y Y Y to restrict the ions to a given radius around the pore itself. As it is, you're probably underestimating entropic contributions to the free energy. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 sample a flat slice at a given Z, and the reported forces and displacements are along Z. What appears to be the reaction coordinate in our case is the radius from the pore mouth, and one has to sample a set of hemispheres from a series of radius values. Is this at all a possibility? Alex On 3/11/2018 5:37 PM, Alex wrote: Hi all, I am looking at what appears to be a paradox. Consider the following situation: we have a graphene membrane with a single pore of a particular type. The pore is located at (x0, y0, h/2), where h is the box height. The membrane is position-restrained along its perimeter and immersed in a solution of NaCl. The pore is designed to trap anions -- and it does, if you artificially bring an anion close enough to the mouth of the pore and run the simulation at, say, room temp. However, the ions do not bind by themselves. 100s of nanoseconds of simulations with high salt concentrations -- nothing. So, I expect a high barrier associated with ion dehydration when entering the pore. Following Justin's tutorial and generating a total of 30 1A-spaced configs (15 below h/2, 15 above h/2) along (x0,y0), gmx wham yields a 6.5 kJ/mol barrier, which isn't high at all! Just from the pullf data when generating the configs (pull along Z with x and y restrained), the naive integral of the pulling force prior to overcoming the hydration barrier yields 4 kJ/mol -- consistent with the WHAM result. But in reality, ions (which aren't restrained around (x0,y0) are not observed to bind, which brings us to my question... It looks like when an ion approaches the pore parallel to the membrane normal, the barrier is indeed low, while approach at an angle yields higher barriers. It appears that WHAM produces the free energy curve resulting from frequent sampling approach directions that have the lowest possible barrier. Is it possible to modify this calculation to give equal weight to all approach directions? Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.