RE: [gmx-users] To get PMF using pull geometry of cylinder
I see. That makes things clear. Thank you so much! -Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 1:09 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: > Ah...Sorry if I confused you. Actually what I meant is if I set the pull > code, e.g., as: > pull_geometry = position > pull_dim = N N Y > pull_rate1 = 0.1 > pull_init1 = 3.0 > pull_vec1 = 0 0 1 > (where pull rate is NOT zero) > Then the position = pull_init + time*pull_rate*pull_vec1 and since pull_vec1 > is z-component-positive (0, 0, 1), the position between the reference and the > pull group increases monotonically and that's not what I want. I want the > distance to decrease so the pull_vec1 should be (0,0,-1). Am I right? > If you want the two species to approach rather than separate, do not change the pull_vec, change the pull_rate so that it is less than zero. A negative pull_rate will decrease the separation over time. Note that pull_dim is irrelevant for pull_geometry=position; only pull_vec1 is required. -Justin > Thanks, > Dejun > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Justin A. Lemkul [jalem...@vt.edu] > Sent: Thursday, May 26, 2011 11:26 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder > > Lin, Dejun wrote: >> Thank you Justin. But I'm still confused about the pull_vec1. Is the vector >> pointing from the reference or from the pull group for all the geometry >> settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, >> pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = >> pull_init + time*pull_rate*pull_vec1 according to the manual and it's >> actually pulling the pull group away from the reference because the vector >> has a positive z component. >> > > The reference group serves as the reference :) Thus, the vector connecting > your > reference and pull group is (0,0,1) since the pull group has a larger > z-coordinate. You're right about the position equation, but you've got a > pull_rate1 of zero, so the added term drops out and position = pull_init1. > >> BTW, I did consider using position geometry but can I get the PMF using >> pull_rate NOT equal to zero? The reason I turned to cylinder is that with >> "distance" geometry the membrane concaved as the micelle was restrained to a >> very short distance (any distance below the critical distance where the >> fusion was supposed to occur) without fusing and this would persist for some >> hundred nanoseconds. >> > > To obtain the PMF, the pull rate should be zero, using several (many) > independent simulations along the desired reaction coordinate. See the > tutorial: > > http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling > > -Justin > >> Thanks again for your help! Dejun >> >> ________________________ From: gmx-users-boun...@gromacs.org >> [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul >> [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list >> for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of >> cylinder >> >> Lin, Dejun wrote: >>> Hi all, >>> >>> I want to do an umbrella sampling to calculate the potential of mean force >>> of a micelle fusing to a lipid membrane. In the starting configuration, the >>> membrane normal is set in z direction and the membrane is under the >>> micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used >>> pull_geometry = distance but the sampling took to long to converge. And >>> then I considered using cylinder instead and set up the pull code as: pull >>> = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = >>> no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle >>> pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 >>> = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 >>> pull_nstfout = 1000 >>> >>> And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. >>> 23.3397 4.90267 100. 0.7424261.86002 >>> 200.0.7378421.86232 300. >>> 0.7626411.83985 400.
Re: [gmx-users] To get PMF using pull geometry of cylinder
Lin, Dejun wrote: Ah...Sorry if I confused you. Actually what I meant is if I set the pull code, e.g., as: pull_geometry = position pull_dim = N N Y pull_rate1 = 0.1 pull_init1 = 3.0 pull_vec1 = 0 0 1 (where pull rate is NOT zero) Then the position = pull_init + time*pull_rate*pull_vec1 and since pull_vec1 is z-component-positive (0, 0, 1), the position between the reference and the pull group increases monotonically and that's not what I want. I want the distance to decrease so the pull_vec1 should be (0,0,-1). Am I right? If you want the two species to approach rather than separate, do not change the pull_vec, change the pull_rate so that it is less than zero. A negative pull_rate will decrease the separation over time. Note that pull_dim is irrelevant for pull_geometry=position; only pull_vec1 is required. -Justin Thanks, Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 11:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Thank you Justin. But I'm still confused about the pull_vec1. Is the vector pointing from the reference or from the pull group for all the geometry settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = pull_init + time*pull_rate*pull_vec1 according to the manual and it's actually pulling the pull group away from the reference because the vector has a positive z component. The reference group serves as the reference :) Thus, the vector connecting your reference and pull group is (0,0,1) since the pull group has a larger z-coordinate. You're right about the position equation, but you've got a pull_rate1 of zero, so the added term drops out and position = pull_init1. BTW, I did consider using position geometry but can I get the PMF using pull_rate NOT equal to zero? The reason I turned to cylinder is that with "distance" geometry the membrane concaved as the micelle was restrained to a very short distance (any distance below the critical distance where the fusion was supposed to occur) without fusing and this would persist for some hundred nanoseconds. To obtain the PMF, the pull rate should be zero, using several (many) independent simulations along the desired reaction coordinate. See the tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin Thanks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100. 0.7424261.86002 200.0.7378421.86232 300. 0.7626411.83985 400.21.6814 1.86777 500.0.771017 1.82482 600. 0.7890361.83254 700.0.793745 1.83503 800. 0.804732 1.84217 900. 0.80137 1.84166 1000. 0.8179791.83546 1100. 0.8062721.83535 1200. 0.792355 1.80372 1300. 0.786839 1.8438 1400. 0.798686 1.82625 1500. 0.8028591.84138 1600. 0.803844 1.84379 (pf.xvg) 100. -480.158 200. -498.547 300. -318.839 400. -542.14 500. -198.526 600. -260.291 700. -280.22 800. -337.385 900. -333.317 1000. -283.644 1100. -282.761 1200. -29.7684 1300.-350.409 1400. -209.991 1500. -331.029 1600. -350.309 And I visualized the trajectory in VMD and found that an "explosion" of the micelle
RE: [gmx-users] To get PMF using pull geometry of cylinder
Ah...Sorry if I confused you. Actually what I meant is if I set the pull code, e.g., as: pull_geometry = position pull_dim = N N Y pull_rate1 = 0.1 pull_init1 = 3.0 pull_vec1 = 0 0 1 (where pull rate is NOT zero) Then the position = pull_init + time*pull_rate*pull_vec1 and since pull_vec1 is z-component-positive (0, 0, 1), the position between the reference and the pull group increases monotonically and that's not what I want. I want the distance to decrease so the pull_vec1 should be (0,0,-1). Am I right? Thanks, Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 11:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: > Thank you Justin. But I'm still confused about the pull_vec1. Is the vector > pointing from the reference or from the pull group for all the geometry > settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, > pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = > pull_init + time*pull_rate*pull_vec1 according to the manual and it's > actually pulling the pull group away from the reference because the vector > has a positive z component. > The reference group serves as the reference :) Thus, the vector connecting your reference and pull group is (0,0,1) since the pull group has a larger z-coordinate. You're right about the position equation, but you've got a pull_rate1 of zero, so the added term drops out and position = pull_init1. > BTW, I did consider using position geometry but can I get the PMF using > pull_rate NOT equal to zero? The reason I turned to cylinder is that with > "distance" geometry the membrane concaved as the micelle was restrained to a > very short distance (any distance below the critical distance where the > fusion was supposed to occur) without fusing and this would persist for some > hundred nanoseconds. > To obtain the PMF, the pull rate should be zero, using several (many) independent simulations along the desired reaction coordinate. See the tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin > Thanks again for your help! Dejun > > From: gmx-users-boun...@gromacs.org > [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul > [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list > for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of > cylinder > > Lin, Dejun wrote: >> Hi all, >> >> I want to do an umbrella sampling to calculate the potential of mean force >> of a micelle fusing to a lipid membrane. In the starting configuration, the >> membrane normal is set in z direction and the membrane is under the >> micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used >> pull_geometry = distance but the sampling took to long to converge. And >> then I considered using cylinder instead and set up the pull code as: pull >> = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = >> no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle >> pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 >> = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 >> pull_nstfout = 1000 >> >> And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. >> 23.3397 4.90267 100. 0.7424261.86002 >> 200.0.7378421.86232 300. >> 0.7626411.83985 400.21.6814 >> 1.86777 500.0.771017 1.82482 600. >> 0.7890361.83254 700.0.793745 >> 1.83503 800. 0.804732 1.84217 900. >> 0.80137 1.84166 1000. 0.8179791.83546 >> 1100. 0.8062721.83535 1200. 0.792355 >> 1.80372 1300. 0.786839 1.8438 1400. 0.798686 >> 1.82625 1500. 0.8028591.84138 1600. 0.803844 >> 1.84379 >> >> (pf.xvg) 100. -480.158 200. -498.547 >> 300. -318.839 400. -542.14 500. >> -198.526 600. -260.291 700. -280.22 >> 800. -337.385 900. -333.317 1000. -283.644 >> 1100. -282.761 1200. -29.7684 1300.-350.409 1400. >> -209.991 1500. -331.029 1600. -350.309 >> >> And I v
Re: [gmx-users] To get PMF using pull geometry of cylinder
Lin, Dejun wrote: Thank you Justin. But I'm still confused about the pull_vec1. Is the vector pointing from the reference or from the pull group for all the geometry settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = pull_init + time*pull_rate*pull_vec1 according to the manual and it's actually pulling the pull group away from the reference because the vector has a positive z component. The reference group serves as the reference :) Thus, the vector connecting your reference and pull group is (0,0,1) since the pull group has a larger z-coordinate. You're right about the position equation, but you've got a pull_rate1 of zero, so the added term drops out and position = pull_init1. BTW, I did consider using position geometry but can I get the PMF using pull_rate NOT equal to zero? The reason I turned to cylinder is that with "distance" geometry the membrane concaved as the micelle was restrained to a very short distance (any distance below the critical distance where the fusion was supposed to occur) without fusing and this would persist for some hundred nanoseconds. To obtain the PMF, the pull rate should be zero, using several (many) independent simulations along the desired reaction coordinate. See the tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin Thanks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100. 0.7424261.86002 200.0.7378421.86232 300. 0.7626411.83985 400.21.6814 1.86777 500.0.771017 1.82482 600. 0.7890361.83254 700.0.793745 1.83503 800. 0.804732 1.84217 900. 0.80137 1.84166 1000. 0.8179791.83546 1100. 0.8062721.83535 1200. 0.792355 1.80372 1300. 0.786839 1.8438 1400. 0.798686 1.82625 1500. 0.8028591.84138 1600. 0.803844 1.84379 (pf.xvg) 100. -480.158 200. -498.547 300. -318.839 400. -542.14 500. -198.526 600. -260.291 700. -280.22 800. -337.385 900. -333.317 1000. -283.644 1100. -282.761 1200. -29.7684 1300.-350.409 1400. -209.991 1500. -331.029 1600. -350.309 And I visualized the trajectory in VMD and found that an "explosion" of the micelle (with all its residues scattered in the box). I then changed the pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the "explosion" was gone and everything seemed to work. But I'm not quite sure if I'm setting up the pull-code right because if z(COM-membrane) < z(COM-micelle), then pull_vec1 = 0.0 0.0 -1.0 should be the right choice. Basically, I think my The negative is incorrect. If the micelle is "above" the membrane (i.e., it has a greater z-coordinate), then the reference vector should be positive with respect to the reference position. It would appear from the pullx.xvg file that you've got some weird PBC crossing going on, since the reference positions oscillate dramatically at the beginning of the simulation. pull-code is restraining the COM of the micelle to the COM of a "cylinder" of the membrane at a distance of 1.8nm, with the vector pointing from COM(micelle) to COM(cylinder) being (0,0,-1). So can anyone explain what caused the explosion or am I setting up the pull-code right? And what are the 2nd and 3rd column in the px.xvg output in this case? For such a
RE: [gmx-users] To get PMF using pull geometry of cylinder
Thank you Justin. But I'm still confused about the pull_vec1. Is the vector pointing from the reference or from the pull group for all the geometry settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = pull_init + time*pull_rate*pull_vec1 according to the manual and it's actually pulling the pull group away from the reference because the vector has a positive z component. BTW, I did consider using position geometry but can I get the PMF using pull_rate NOT equal to zero? The reason I turned to cylinder is that with "distance" geometry the membrane concaved as the micelle was restrained to a very short distance (any distance below the critical distance where the fusion was supposed to occur) without fusing and this would persist for some hundred nanoseconds. Thanks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: > Hi all, > > I want to do an umbrella sampling to calculate the potential of mean force of > a micelle fusing to a lipid membrane. In the starting configuration, the > membrane normal is set in z direction and the membrane is under the micelle > (z(COM-membrane) < z(COM-micelle)). At the beginning, I used pull_geometry = > distance but the sampling took to long to converge. And then I considered > using cylinder instead and set up the pull code as: pull = > umbrella > pull_geometry = cylinder pull_dim = N N Y pull_start = no > pull_ngroups = 1 > pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 > pull_r1 > = 2.3 pull_r0 = 2.5 pull_init1= 1.8 pull_rate1= 0.0 > pull_k1 = 1000 > pull_nstxout = 1000 pull_nstfout = 1000 > > And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. > 23.3397 > 4.90267 100. 0.7424261.86002 200. > 0.7378421.86232 > 300. 0.7626411.83985 400. > 21.6814 1.86777 500.0.771017 > 1.82482 600. 0.7890361.83254 700. > 0.7937451.83503 800. > 0.804732 1.84217 900.0.80137 1.84166 > 1000. 0.8179791.83546 > 1100. 0.8062721.83535 1200. 0.792355 > 1.80372 1300. 0.786839 > 1.8438 1400. 0.7986861.82625 1500. > 0.8028591.84138 1600. > 0.803844 1.84379 > > (pf.xvg) 100. -480.158 200. -498.547 > 300. -318.839 400. > -542.14 500. -198.526 600. -260.291 > 700. -280.22 800. > -337.385 900. -333.317 1000. -283.644 1100. > -282.761 1200. > -29.7684 1300.-350.409 1400. -209.991 1500. > -331.029 1600. > -350.309 > > And I visualized the trajectory in VMD and found that an "explosion" of the > micelle (with all its residues scattered in the box). I then changed the > pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the "explosion" > was > gone and everything seemed to work. But I'm not quite sure if I'm setting up > the pull-code right because if z(COM-membrane) < z(COM-micelle), then > pull_vec1 = 0.0 0.0 -1.0 should be the right choice. Basically, I think my The negative is incorrect. If the micelle is "above" the membrane (i.e., it has a greater z-coordinate), then the reference vector should be positive with respect to the reference position. It would appear from the pullx.xvg file that you've got some weird PBC crossing going on, since the reference positions oscillate dramatically at the beginning of the simulation. > pull-code is restraining the COM of the micelle to the COM of a "cylinder" of > the membrane at a distance of 1.8nm, with the vector pointing from > COM(micelle) to COM(cylinder) being (0,0,-1). So can anyone explain what > caused the explosion or am I setting up the pull-code right? And what are the > 2nd and 3rd column in the px.xvg output in this case? > For such a simple restraint, I don't think there is any need for cylinder geometry. You're not using different weighting. Any of the other
Re: [gmx-users] To get PMF using pull geometry of cylinder
Lin, Dejun wrote: Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100.0.7424261.86002 200. 0.7378421.86232 300. 0.7626411.83985 400. 21.6814 1.86777 500.0.771017 1.82482 600.0.7890361.83254 700. 0.7937451.83503 800. 0.804732 1.84217 900. 0.80137 1.84166 1000. 0.817979 1.83546 1100. 0.806272 1.83535 1200. 0.792355 1.80372 1300. 0.786839 1.8438 1400.0.7986861.82625 1500. 0.8028591.84138 1600. 0.8038441.84379 (pf.xvg) 100. -480.158 200. -498.547 300. -318.839 400. -542.14 500.-198.526 600. -260.291 700. -280.22 800. -337.385 900. -333.317 1000. -283.644 1100. -282.761 1200. -29.7684 1300. -350.409 1400. -209.991 1500. -331.029 1600. -350.309 And I visualized the trajectory in VMD and found that an "explosion" of the micelle (with all its residues scattered in the box). I then changed the pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the "explosion" was gone and everything seemed to work. But I'm not quite sure if I'm setting up the pull-code right because if z(COM-membrane) < z(COM-micelle), then pull_vec1 = 0.0 0.0 -1.0 should be the right choice. Basically, I think my The negative is incorrect. If the micelle is "above" the membrane (i.e., it has a greater z-coordinate), then the reference vector should be positive with respect to the reference position. It would appear from the pullx.xvg file that you've got some weird PBC crossing going on, since the reference positions oscillate dramatically at the beginning of the simulation. pull-code is restraining the COM of the micelle to the COM of a "cylinder" of the membrane at a distance of 1.8nm, with the vector pointing from COM(micelle) to COM(cylinder) being (0,0,-1). So can anyone explain what caused the explosion or am I setting up the pull-code right? And what are the 2nd and 3rd column in the px.xvg output in this case? For such a simple restraint, I don't think there is any need for cylinder geometry. You're not using different weighting. Any of the other pull_geometry settings should work, with "distance" probably being the most intuitive. I suspect it would be very easy to use the "position" setting as well. The output in the pullx.xvg file should be labeled in the header. The generic output is (x,y,z) of the reference group, followed by delta(x,y,z) for the restrained group, i.e. how far away the restrained group is along each coordinate axis. If you're only restraining/pulling along the z-axis, then the only terms written are z and dz, since, in principle, x, y, dx, and dy are all fixed, with the last two terms being zero. -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
[gmx-users] To get PMF using pull geometry of cylinder
Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull= umbrella pull_geometry = cylinder pull_dim= N N Y pull_start = no pull_ngroups= 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 = 1.8 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout= 1000 pull_nstfout= 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100.0.7424261.86002 200.0.7378421.86232 300.0.7626411.83985 400.21.6814 1.86777 500.0.7710171.82482 600.0.7890361.83254 700.0.7937451.83503 800.0.8047321.84217 900.0.80137 1.84166 1000. 0.8179791.83546 1100. 0.8062721.83535 1200. 0.7923551.80372 1300. 0.7868391.8438 1400. 0.7986861.82625 1500. 0.8028591.84138 1600. 0.8038441.84379 (pf.xvg) 100.-480.158 200.-498.547 300.-318.839 400.-542.14 500.-198.526 600.-260.291 700.-280.22 800.-337.385 900.-333.317 1000. -283.644 1100. -282.761 1200. -29.7684 1300. -350.409 1400. -209.991 1500. -331.029 1600. -350.309 And I visualized the trajectory in VMD and found that an "explosion" of the micelle (with all its residues scattered in the box). I then changed the pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the "explosion" was gone and everything seemed to work. But I'm not quite sure if I'm setting up the pull-code right because if z(COM-membrane) < z(COM-micelle), then pull_vec1 = 0.0 0.0 -1.0 should be the right choice. Basically, I think my pull-code is restraining the COM of the micelle to the COM of a "cylinder" of the membrane at a distance of 1.8nm, with the vector pointing from COM(micelle) to COM(cylinder) being (0,0,-1). So can anyone explain what caused the explosion or am I setting up the pull-code right? And what are the 2nd and 3rd column in the px.xvg output in this case? Thanks, Dejun -- 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
