Re: [gmx-users] Pull code vs. manual pull for umbrella sampling
Hello, As I had explained earlier, I have done MD at varied protein bi-layer distances. I now want to create a probability distribution histogram along the reaction coordinate I generated by varying the distances. I know I can concatenate various .trr files I have from various MD runs with different initial starting configurations. Is there a way to obtain the probability distribution histogram. Kindly help. Thanks, sxn Shivangi Nangia, Ph. D Postdoctoral Research Associate Department of Molecular and Cell Biology University of Connecticut On Fri, Jan 24, 2014 at 3:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/24/14, 3:50 PM, shivangi nangia wrote: Dear Justin, Okay, so I have multiple configurations of protein and bi-layer system (30 initial configurations) at varied distances (in steps of 0.05 nm). The protein has been moved away with respect to its COM. So I have manually pulled the protein away from the bi-layer instead of using the pull code. I have run MD simulations for each of these configurations. I need to use g_wham to calculate the PMF and for that I need the pullx.xvg files. It won't be possible. What you did wasn't umbrella sampling, it was just MD. If there is no restraint potential applied during the simulations in each of the sampling windows, there's nothing to de-bias to reconstruct a free energy profile. You can generate the configurations in any manner you like (manually or by using the pull code), but the umbrella sampling itself requires the use of the pull code. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pull code vs. manual pull for umbrella sampling
On 1/27/14, 3:49 PM, shivangi nangia wrote: Hello, As I had explained earlier, I have done MD at varied protein bi-layer distances. I now want to create a probability distribution histogram along the reaction coordinate I generated by varying the distances. I know I can concatenate various .trr files I have from various MD runs with different initial starting configurations. There is no need to concatenate trajectories. In fact, that will probably make your life harder having one massive trajectory. I suspect you'll want the distributions from each individual trajectory, anyway. Is there a way to obtain the probability distribution histogram. That's what g_analyze -distr does. Feed it the output of g_dist. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Pull code vs. manual pull for umbrella sampling
Hello, I wish to perform umbrella sampling without using the pull code. I have varied starting configurations for protein-bilayer. Is there any advantage(s) of doing a manual pull versus the pull code or vice-versa? What is the reason to do it with pull force? Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pull code vs. manual pull for umbrella sampling
On 1/24/14, 2:34 PM, shivangi nangia wrote: Hello, I wish to perform umbrella sampling without using the pull code. I have varied starting configurations for protein-bilayer. Is there any advantage(s) of doing a manual pull versus the pull code or vice-versa? What is the reason to do it with pull force? I think you need to provide more detail on what you are doing or are planning to do. What is manual pulling? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pull code vs. manual pull for umbrella sampling
Dear Justin, Okay, so I have multiple configurations of protein and bi-layer system (30 initial configurations) at varied distances (in steps of 0.05 nm). The protein has been moved away with respect to its COM. So I have manually pulled the protein away from the bi-layer instead of using the pull code. I have run MD simulations for each of these configurations. I need to use g_wham to calculate the PMF and for that I need the pullx.xvg files. Thanks, sxn Shivangi Nangia, Ph. D Postdoctoral Research Associate Department of Molecular and Cell Biology University of Connecticut On Fri, Jan 24, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/24/14, 2:34 PM, shivangi nangia wrote: Hello, I wish to perform umbrella sampling without using the pull code. I have varied starting configurations for protein-bilayer. Is there any advantage(s) of doing a manual pull versus the pull code or vice-versa? What is the reason to do it with pull force? I think you need to provide more detail on what you are doing or are planning to do. What is manual pulling? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
