Re: [gmx-users] umbrella sampling-Bimodal Histograms
I took initial 300 as equilibration,Now it seems fine. Thank you .. On Tue, Jun 22, 2010 at 9:21 AM, chris.ne...@utoronto.ca wrote: Take that replica on the left that shows a bimodal histogram. Now plot a time series of the displacement: x-axis = time and y-axis = displacement along reaction coord. Is it jumping back and forth between two regions of sampling? Probably not... more likely it starts near one maximum and transitions to another maximum. If this is true then it simply means that you have not equilibrated enough. Run longer and cut some of the initial sampling. Chris. -- original message -- I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 40). Pull_init will vary for each frame, depends on the window spacing. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVlhl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, chris.neale at utoronto.ca wrote: Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction coordinate? My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at those times yet. Your Fc is fine. Post your pull settings. Chris. -- original message -- When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella sampling-Bimodal Histograms
Hi Friends, When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? Thanks, -- Aswathy -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella sampling-Bimodal Histograms
Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction coordinate? My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at those times yet. Your Fc is fine. Post your pull settings. Chris. -- original message -- When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] umbrella sampling-Bimodal Histograms
I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 40). Pull_init will vary for each frame, depends on the window spacing. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVlhl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, chris.ne...@utoronto.ca wrote: Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction coordinate? My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at those times yet. Your Fc is fine. Post your pull settings. Chris. -- original message -- When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella sampling-Bimodal Histograms
Take that replica on the left that shows a bimodal histogram. Now plot a time series of the displacement: x-axis = time and y-axis = displacement along reaction coord. Is it jumping back and forth between two regions of sampling? Probably not... more likely it starts near one maximum and transitions to another maximum. If this is true then it simply means that you have not equilibrated enough. Run longer and cut some of the initial sampling. Chris. -- original message -- I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 40). Pull_init will vary for each frame, depends on the window spacing. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVlhl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, chris.neale at utoronto.ca wrote: Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction coordinate? My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at those times yet. Your Fc is fine. Post your pull settings. Chris. -- original message -- When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
