Re: [gmx-users] Re: distance/direction PMF
Hi Justin I think what is happening is that grompp is returning the projection of the current vector between the two reference groups onto the stated vector in the mdp file. i.e the dot product of the two vectors. The resulting PMF plot must therefore be a function of this varying cross product. I say varying as I don't think the dynamics constrain the pull group alone that vector alone. When you change the vector in the mdp file to be that of the new vector connecting the two groups grompp gives the actual distance between the two groups. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Yeah I set pull_init =0, and pull_start = yes, and it still gave a distance at start as 0.78nm. It must be doing something funny because with pull_vec, because when I use pull_geometry = distance and pull_dim = Y Y Y, the distance 0.815nm is returned as the distance at start, which is the actual distance between the two groups. I have no idea why this is happening. If you'd like me to troubleshoot further and see if I can get to the bottom of this, please send me (off-list is OK): 1. Coordinate file 2. Topology file(s) 3. The .mdp file that is giving the weird result -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start that grompp returns is also 0.78nm, even though the actual distance is 0.815nm. That's why I was asking what this distance actually means, as it is not the absolute distance between the reference groups. As I said before, you're telling grompp to make that the reference distance. You say the specified distance in the mdp file is 0.78 nm, therefore grompp is doing what it's told. If that's not the desired distance, then don't set it as such. Have you tried the combination I suggested in the last message? Does it give an initial distance of 0.815 nm? Also as regards to your second point; what if in the initial configurations the two reference groups do not lie along the stated vector? Hard to say, but probably you'll get some very high forces at the outset of the simulation as the simulation as the umbrella potential tries to force the pulled group to conform to the restraint specifications. Whether or not that negatively impacts the ultimate result of the simulation is also an important consideration. If you're pulling along a given vector, you should start with your reference coordinates as close to the desired location as possible. -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ? You're telling grompp that the initial distance is 0.78 nm, so it's spitting that back out. If that's not the true distance, then specify the correct quantity :) The distance should be correctly detected with: pull_start = yes pull_init = 0 As for the second question, the vector doesn't change over the simulation, but the position of pull_group1 along that vector will. That's what the umbrella potential is doing - it allows for harmonic oscillation along any of the dimensions specified by pull_vec/pull_dim (depending on the settings). -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: distance/direction PMF
Gavin Melaugh wrote: Hi all Could someone please get back to me on this. I have ran two sets of umbrella sampling simulations 1- Using pull_geometry = distance, and pull_dim = Y Y Y 2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125 0.735968 In both cases I wish to calculate the PMF for taking a host out of a guest. I specify the distance between the COM of the two groups in the respective mdp files. The two curves I get are completely different which has leads me to ask a couple of questions: You're doing two different things here, so I'd suspect that you're going to get a different answer with different settings. 1) Does the vector change as the dynamics evolves (i.e is it just relative between the two points) or does it remain fixed in space? It is relative. 2) Using umbrella sampling in the second case does the relative position of the pull group (guest) fluctuate about the distance along the specified vector? Yes. Note- I couldn't run g_wham with pull_geometry = direction in my current version of gromacs, so I ran it in 4.5.3 but I had to use the -if pullf-files.xvg option. We'll have to assume that your current version is something in the 4.0.x series, so this outcome is expected. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force Some help would be appreciated as I have to be sure of what the program is actually doing. There's always the code :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: distance/direction PMF
Gavin Melaugh wrote: Hi Justin Many thanks for the reply I know technically I am doing two different things. However due to my starting conifgurations in both cases I would expect similar results. Could you confirm the following points 1) In pull_geometry=distance, and pull_dim =YYY; is the absolute distance between the COM of both groups in all directions considered ? Yes. 2) In pull_geometry = direction, with a specified vector; I assume that it is the distance between the two groups along this vector that is considered? Should be. Compare the output of g_dist with what grompp reports as the initial distance. 3) Is the specified vector taken to be the vector connecting the two points? Therefore are the desired distances in the mdp files essentially the magnitudes of this vector at each window. Per the documentation, grompp normalizes the vector, so no, not directly. But if you have proper settings for pull_init/pull_start, then the reference distance should be correctly calculated along the specified vector for each window. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: distance/direction PMF
Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ? Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Many thanks for the reply I know technically I am doing two different things. However due to my starting conifgurations in both cases I would expect similar results. Could you confirm the following points 1) In pull_geometry=distance, and pull_dim =YYY; is the absolute distance between the COM of both groups in all directions considered ? Yes. 2) In pull_geometry = direction, with a specified vector; I assume that it is the distance between the two groups along this vector that is considered? Should be. Compare the output of g_dist with what grompp reports as the initial distance. 3) Is the specified vector taken to be the vector connecting the two points? Therefore are the desired distances in the mdp files essentially the magnitudes of this vector at each window. Per the documentation, grompp normalizes the vector, so no, not directly. But if you have proper settings for pull_init/pull_start, then the reference distance should be correctly calculated along the specified vector for each window. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: distance/direction PMF
Gavin Melaugh wrote: Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ? You're telling grompp that the initial distance is 0.78 nm, so it's spitting that back out. If that's not the true distance, then specify the correct quantity :) The distance should be correctly detected with: pull_start = yes pull_init = 0 As for the second question, the vector doesn't change over the simulation, but the position of pull_group1 along that vector will. That's what the umbrella potential is doing - it allows for harmonic oscillation along any of the dimensions specified by pull_vec/pull_dim (depending on the settings). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: distance/direction PMF
Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start that grompp returns is also 0.78nm, even though the actual distance is 0.815nm. That's why I was asking what this distance actually means, as it is not the absolute distance between the reference groups. Also as regards to your second point; what if in the initial configurations the two reference groups do not lie along the stated vector? Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ? You're telling grompp that the initial distance is 0.78 nm, so it's spitting that back out. If that's not the true distance, then specify the correct quantity :) The distance should be correctly detected with: pull_start = yes pull_init = 0 As for the second question, the vector doesn't change over the simulation, but the position of pull_group1 along that vector will. That's what the umbrella potential is doing - it allows for harmonic oscillation along any of the dimensions specified by pull_vec/pull_dim (depending on the settings). -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: distance/direction PMF
Gavin Melaugh wrote: Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start that grompp returns is also 0.78nm, even though the actual distance is 0.815nm. That's why I was asking what this distance actually means, as it is not the absolute distance between the reference groups. As I said before, you're telling grompp to make that the reference distance. You say the specified distance in the mdp file is 0.78 nm, therefore grompp is doing what it's told. If that's not the desired distance, then don't set it as such. Have you tried the combination I suggested in the last message? Does it give an initial distance of 0.815 nm? Also as regards to your second point; what if in the initial configurations the two reference groups do not lie along the stated vector? Hard to say, but probably you'll get some very high forces at the outset of the simulation as the simulation as the umbrella potential tries to force the pulled group to conform to the restraint specifications. Whether or not that negatively impacts the ultimate result of the simulation is also an important consideration. If you're pulling along a given vector, you should start with your reference coordinates as close to the desired location as possible. -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ? You're telling grompp that the initial distance is 0.78 nm, so it's spitting that back out. If that's not the true distance, then specify the correct quantity :) The distance should be correctly detected with: pull_start = yes pull_init = 0 As for the second question, the vector doesn't change over the simulation, but the position of pull_group1 along that vector will. That's what the umbrella potential is doing - it allows for harmonic oscillation along any of the dimensions specified by pull_vec/pull_dim (depending on the settings). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: distance/direction PMF
Yeah I set pull_init =0, and pull_start = yes, and it still gave a distance at start as 0.78nm. It must be doing something funny because with pull_vec, because when I use pull_geometry = distance and pull_dim = Y Y Y, the distance 0.815nm is returned as the distance at start, which is the actual distance between the two groups. Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start that grompp returns is also 0.78nm, even though the actual distance is 0.815nm. That's why I was asking what this distance actually means, as it is not the absolute distance between the reference groups. As I said before, you're telling grompp to make that the reference distance. You say the specified distance in the mdp file is 0.78 nm, therefore grompp is doing what it's told. If that's not the desired distance, then don't set it as such. Have you tried the combination I suggested in the last message? Does it give an initial distance of 0.815 nm? Also as regards to your second point; what if in the initial configurations the two reference groups do not lie along the stated vector? Hard to say, but probably you'll get some very high forces at the outset of the simulation as the simulation as the umbrella potential tries to force the pulled group to conform to the restraint specifications. Whether or not that negatively impacts the ultimate result of the simulation is also an important consideration. If you're pulling along a given vector, you should start with your reference coordinates as close to the desired location as possible. -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ? You're telling grompp that the initial distance is 0.78 nm, so it's spitting that back out. If that's not the true distance, then specify the correct quantity :) The distance should be correctly detected with: pull_start = yes pull_init = 0 As for the second question, the vector doesn't change over the simulation, but the position of pull_group1 along that vector will. That's what the umbrella potential is doing - it allows for harmonic oscillation along any of the dimensions specified by pull_vec/pull_dim (depending on the settings). -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: distance/direction PMF
Gavin Melaugh wrote: Yeah I set pull_init =0, and pull_start = yes, and it still gave a distance at start as 0.78nm. It must be doing something funny because with pull_vec, because when I use pull_geometry = distance and pull_dim = Y Y Y, the distance 0.815nm is returned as the distance at start, which is the actual distance between the two groups. I have no idea why this is happening. If you'd like me to troubleshoot further and see if I can get to the bottom of this, please send me (off-list is OK): 1. Coordinate file 2. Topology file(s) 3. The .mdp file that is giving the weird result -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start that grompp returns is also 0.78nm, even though the actual distance is 0.815nm. That's why I was asking what this distance actually means, as it is not the absolute distance between the reference groups. As I said before, you're telling grompp to make that the reference distance. You say the specified distance in the mdp file is 0.78 nm, therefore grompp is doing what it's told. If that's not the desired distance, then don't set it as such. Have you tried the combination I suggested in the last message? Does it give an initial distance of 0.815 nm? Also as regards to your second point; what if in the initial configurations the two reference groups do not lie along the stated vector? Hard to say, but probably you'll get some very high forces at the outset of the simulation as the simulation as the umbrella potential tries to force the pulled group to conform to the restraint specifications. Whether or not that negatively impacts the ultimate result of the simulation is also an important consideration. If you're pulling along a given vector, you should start with your reference coordinates as close to the desired location as possible. -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ? You're telling grompp that the initial distance is 0.78 nm, so it's spitting that back out. If that's not the true distance, then specify the correct quantity :) The distance should be correctly detected with: pull_start = yes pull_init = 0 As for the second question, the vector doesn't change over the simulation, but the position of pull_group1 along that vector will. That's what the umbrella potential is doing - it allows for harmonic oscillation along any of the dimensions specified by pull_vec/pull_dim (depending on the settings). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
