[gmx-users] About g_msd. I want to plot the curve from 0.01ps.
Hi I have been learning how to use gromacs owing to your advice. I have simple question on g_msd. I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD curve from 0.01ps to the last of simulation (my case, 1ns). However, g_msd always produce the MSD curve starting from 1ps. How can I adjust the instance of starting time of MSD curve (for example, 0.01ps - 1ns)?? please help me. Have a nice day! -- 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] About g_msd. I want to plot the curve from 0.01ps.
On 10/01/2012 11:21 PM, Kiwoong Kim wrote: Hi I have been learning how to use gromacs owing to your advice. I have simple question on g_msd. I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD curve from 0.01ps to the last of simulation (my case, 1ns). However, g_msd always produce the MSD curve starting from 1ps. How can I adjust the instance of starting time of MSD curve (for example, 0.01ps - 1ns)?? It can't analyze more frames than exist in your trajectory file, which you controlled with your .mdp file when you ran the simulation. See what gmxcheck has to say about your trajectory file. Mark -- 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] About g_msd. I want to plot the curve from 0.01ps.
Kiwoong Kim wrote: Hi I have been learning how to use gromacs owing to your advice. I have simple question on g_msd. I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD curve from 0.01ps to the last of simulation (my case, 1ns). However, g_msd always produce the MSD curve starting from 1ps. How can I adjust the instance of starting time of MSD curve (for example, 0.01ps - 1ns)?? Please read g_msd -h, with particular attention to the section on -beginfit and -endfit. -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] About g_msd
Hi Justin, Wohlert and Edholm (http://dx.doi.org/10.1063/1.2393240) suggested to extract the motion of the 2 monolayers relative to each other, before calculating the MSD. This is an artefact coming from the finite size of computer simulations. This may explain the discrepancy you get between both leaflets. Second, they showed that there are two different diffusions. A fast diffusion occuring on ps time scale and a longer one which is brownian and can be compared to FRAP experiments. In their paper, they propose a fitting procedure that extracts both diffusion constants. Furthermore, be sure to equilibrate enough (a few tens of ns) before doing this analysis. Cheers, Patrick Justin A. Lemkul a écrit : Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists
Re: [gmx-users] About g_msd (and noise)
I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end? - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search
Re: [gmx-users] About g_msd (and noise)
Alan Dodd wrote: I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end? DESCRIPTION --- g_msd computes the mean square displacement (MSD) of atoms from their initial positions. This provides an easy way to compute the diffusion constant using the Einstein relation. The time between additional starting points for the MSD calculation is set with -trestart. The diffusion constant is calculated by least squares fitting a straight line through the MSD from -beginfit to -endfit. An error estimate given, which is the difference of the diffusion coefficients obtained from fits over the two halfs of the fit interval. Have you tried these option? - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before
Re: [gmx-users] About g_msd (and noise)
Hi Alan, see Fig 3 in the paper I was mentionning in my previous post (http://dx.doi.org/10.1063/1.2393240); from the legend the authors say 'deviation from linearity at long times is due to poor statistics'. So to answer your question, that's probably true, most papers just show the beginning of the plot where the MSD is linear. As quoted before by David, one has just to take care about fitting in the linear region (with the -beginfit and -endfit flags). Cheers, Patrick Alan Dodd a écrit : I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end? - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] About g_msd
Quoting David van der Spoel [EMAIL PROTECTED]: Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thank you! This appears to be giving me reasonable results. I have several dozen more trajectories to analyze, and will report back if anything goes amiss, but so far it's a good start! -Justin Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department
Re: [gmx-users] About g_msd
Patrick, Thanks for pointing this paper out. I'll have a look at it. As for now, I'm following David's advice and will see where that takes me. -Justin Quoting Patrick Fuchs [EMAIL PROTECTED]: Hi Justin, Wohlert and Edholm (http://dx.doi.org/10.1063/1.2393240) suggested to extract the motion of the 2 monolayers relative to each other, before calculating the MSD. This is an artefact coming from the finite size of computer simulations. This may explain the discrepancy you get between both leaflets. Second, they showed that there are two different diffusions. A fast diffusion occuring on ps time scale and a longer one which is brownian and can be compared to FRAP experiments. In their paper, they propose a fitting procedure that extracts both diffusion constants. Furthermore, be sure to equilibrate enough (a few tens of ns) before doing this analysis. Cheers, Patrick Justin A. Lemkul a écrit : Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http
[gmx-users] About g_msd
Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] About g_msd
What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] About g_msd
Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org
Re: [gmx-users] About g_msd
Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial displacement (within the first several nanoseconds out of 100, likely due to my equilibration procedure of packing the lipids tightly around the peptide), so I attempted to analyze the last 75 ns and 90 ns of the trajectory, using the structures at those times as the reference (in g_msd -s). Still the same result, a large value of D. Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) Thanks again. -Justin Quoting Alan Dodd [EMAIL PROTECTED]: What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface
[gmx-users] About g_msd
Hi all, I have 100-ns trajectories of a membrane protein embedded in a lipid bilayer and I am trying to compute the lateral diffusion coefficients of the lipids in different shells around the protein. Everything was going fine until I re-checked the documentation, at which point I got a little confused. Can someone please help me sort out what I need to do to get the correct lateral diffusion coefficients of my lipids? I have an ordered trajectory (from trjorder), with the lipids ordered according to their distance from the protein. When I issue the command: g_msd -f ../../TrajFiles/ordered.xtc -s ../md.tpr -n ../lipids_shells.ndx -o msd_shells.xvg -ngroup 4 -lateral y -trestart 1000 (and subsequently selecting each of my four index groups) I get output of lateral diffusion coefficients for each group. The index group specified has the lipids by their molecule number, which brings me to my first question: Is that the proper index group to use if I am not specifying -mol? Some of my results come up negative, and I see from the archive from DvdS that this is due to poor single molecule statistics, but I my index file specifies multiple molecules in a shell. I suspect this is a problem with the index file? Do I have to specify the desired group in terms of all the atoms in the lipids of interest? When I issue: g_msd -f ../../TrajFiles/ordered.xtc -s ../md.tpr -n ../lipids_shells.ndx -o msd_shells.xvg -mol msd_mol_shells.xvg -ngroup 4 -lateral y -trestart 1000 (please note the use of the same index file) I get a very different result. The lateral diffusion coefficients in msd_shells.xvg are two orders of magnitude larger than in the first result, and the msd_mol_shells.xvg is filled with mostly 'nan' entries. Is this because of some incompatibility between -ngroup and -mol? I have found in the list archives that the number without the -mol option is more accurate due to statistical sampling, but that seems to contradicts the manual entry for g_msd. Hence my confusion. Thanks in advance for any comments and hints. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
