Re: [gmx-users] Regarding umbrella samplling
On 11/25/14 1:23 AM, Sathish Kumar wrote: Hai gromacs users, Can we use the direction-periodic mdp option while running the samplling of windows instead of distance. The distance option was giving error that Distance of pull group 1 (15.017257 nm) is larger than 0.49 times the box size (15.033495) . So, for all windows can i use the option direction-periodic instead of distance. You can use whatever geometry makes sense. There is no reason to believe that any particular geometry is inherently right or wrong for any given purpose, and generally speaking, if utilized properly, you can usually use any of the geometry options to achieve equivalent effects. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Regarding umbrella samplling
Hai gromacs users, Can we use the direction-periodic mdp option while running the samplling of windows instead of distance. The distance option was giving error that Distance of pull group 1 (15.017257 nm) is larger than 0.49 times the box size (15.033495) . So, for all windows can i use the option direction-periodic instead of distance. Thanks Sathish -- 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] Regarding umbrella samplling
On 10/30/14 1:19 AM, Sathish Kumar wrote: Dear gromacs-users, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Out of the 79 configurations, only for the 78 and 79 configurations while running mdrun i am getting the following error. Fatal error: Distance of pull group 1 (12.277075 nm) is larger than 0.49 times the box size (12.526427) I have used pull geometry = distance How can i solve this problem, please help me in this regard. As described in the tutorial, the pulled distance (when using geometry = distance) cannot exceed half of the box size due to issues related to periodicity of the system. You'll have to decide whether or not you need to be pulling this far, but if you do, you need to set up a larger box. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Regarding umbrella samplling
Dear gromacs-users, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Out of the 79 configurations, only for the 78 and 79 configurations while running mdrun i am getting the following error. Fatal error: Distance of pull group 1 (12.277075 nm) is larger than 0.49 times the box size (12.526427) I have used pull geometry = distance How can i solve this problem, please help me in this regard. Thanks sathish -- 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] Regarding umbrella samplling
Hi. Does that mean the umbrella don't overlap enough at those z ? Can you make an overlay plot of the histograms of each umbrella? On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com wrote: Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Using g_wham, i got the profile.xvg, in that profile.xvg, all PMF values are zero. while running g_wham i am getting warings like below. WARNING, no data point in bin 163 (z=8.27767) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 164 (z=8.31563) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 165 (z=8.35358) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 194 (z=9.45432). Check your histograms! Initialized rapid wham stuff (contrib tolerance 1.31579e-08) Evaluating only 2619 of 15200 expressions. 1) Maximum change 3.178184e+02 100) Maximum change 1.611126e+00 200) Maximum change 3.303540e+00 300) Maximum change 1.239682e+00 400) Maximum change 1.383353e+00 500) Maximum change 1.116406e+00 600) Maximum change 1.241516e+00 700) Maximum change 1.028108e+00 800) Maximum change 1.698508e+00 900) Maximum change 1.331078e+00 Switched to exact iteration in iteration 983 Converged in 984 iterations. Final maximum change 0 Please help me in this regard. Thanks sathish -- 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] Regarding umbrella samplling
Yes, it means what you say. I would decrease the number of bins. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Mon, Oct 13, 2014 at 12:47 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Does that mean the umbrella don't overlap enough at those z ? Can you make an overlay plot of the histograms of each umbrella? On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com wrote: Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Using g_wham, i got the profile.xvg, in that profile.xvg, all PMF values are zero. while running g_wham i am getting warings like below. WARNING, no data point in bin 163 (z=8.27767) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 164 (z=8.31563) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 165 (z=8.35358) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 194 (z=9.45432). Check your histograms! Initialized rapid wham stuff (contrib tolerance 1.31579e-08) Evaluating only 2619 of 15200 expressions. 1) Maximum change 3.178184e+02 100) Maximum change 1.611126e+00 200) Maximum change 3.303540e+00 300) Maximum change 1.239682e+00 400) Maximum change 1.383353e+00 500) Maximum change 1.116406e+00 600) Maximum change 1.241516e+00 700) Maximum change 1.028108e+00 800) Maximum change 1.698508e+00 900) Maximum change 1.331078e+00 Switched to exact iteration in iteration 983 Converged in 984 iterations. Final maximum change 0 Please help me in this regard. Thanks sathish -- 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. -- 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] Regarding umbrella samplling
Hai Yes, I have ploted the histogram, all windows are merged..please check this histo.jpg file attached to the below link. https://www.dropbox.com/s/ndl0w250dnawmib/histogram.jpg?dl=0 On Mon, Oct 13, 2014 at 3:47 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Does that mean the umbrella don't overlap enough at those z ? Can you make an overlay plot of the histograms of each umbrella? On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com wrote: Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Using g_wham, i got the profile.xvg, in that profile.xvg, all PMF values are zero. while running g_wham i am getting warings like below. WARNING, no data point in bin 163 (z=8.27767) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 164 (z=8.31563) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 165 (z=8.35358) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 194 (z=9.45432). Check your histograms! Initialized rapid wham stuff (contrib tolerance 1.31579e-08) Evaluating only 2619 of 15200 expressions. 1) Maximum change 3.178184e+02 100) Maximum change 1.611126e+00 200) Maximum change 3.303540e+00 300) Maximum change 1.239682e+00 400) Maximum change 1.383353e+00 500) Maximum change 1.116406e+00 600) Maximum change 1.241516e+00 700) Maximum change 1.028108e+00 800) Maximum change 1.698508e+00 900) Maximum change 1.331078e+00 Switched to exact iteration in iteration 983 Converged in 984 iterations. Final maximum change 0 Please help me in this regard. Thanks sathish -- 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. -- regards M.SathishKumar -- 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] Regarding umbrella samplling
I am not able to find wheather the windows are overlaped or not. Please help me in this. Thanks. On Mon, Oct 13, 2014 at 10:05 AM, Sathish Kumar sathishk...@gmail.com wrote: Hai Yes, I have ploted the histogram, all windows are merged..please check this histo.jpg file attached to the below link. https://www.dropbox.com/s/ndl0w250dnawmib/histogram.jpg?dl=0 On Mon, Oct 13, 2014 at 3:47 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Does that mean the umbrella don't overlap enough at those z ? Can you make an overlay plot of the histograms of each umbrella? On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com wrote: Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Using g_wham, i got the profile.xvg, in that profile.xvg, all PMF values are zero. while running g_wham i am getting warings like below. WARNING, no data point in bin 163 (z=8.27767) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 164 (z=8.31563) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 165 (z=8.35358) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 194 (z=9.45432). Check your histograms! Initialized rapid wham stuff (contrib tolerance 1.31579e-08) Evaluating only 2619 of 15200 expressions. 1) Maximum change 3.178184e+02 100) Maximum change 1.611126e+00 200) Maximum change 3.303540e+00 300) Maximum change 1.239682e+00 400) Maximum change 1.383353e+00 500) Maximum change 1.116406e+00 600) Maximum change 1.241516e+00 700) Maximum change 1.028108e+00 800) Maximum change 1.698508e+00 900) Maximum change 1.331078e+00 Switched to exact iteration in iteration 983 Converged in 984 iterations. Final maximum change 0 Please help me in this regard. Thanks sathish -- 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. -- regards M.SathishKumar -- regards M.SathishKumar -- 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] Regarding umbrella samplling
On 10/13/14 1:08 PM, Sathish Kumar wrote: I am not able to find wheather the windows are overlaped or not. Please help me in this. You've got a gap in the sampling exactly where g_wham tells you. The histograms show this. You either need more windows or a different force constant, or both. The simplest solution is to add some more windows where you're lacking sampling. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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] Regarding umbrella samplling
Hai I have decreased the number of bins=50 and i have not get the previously mentioned warnings. Still, the profile.xvg is looking like below 2.148184e+000.00e+00 2.300988e+000.00e+00 2.453792e+000.00e+00 2.606596e+000.00e+00 2.759400e+000.00e+00 2.912204e+000.00e+00 3.065009e+000.00e+00 3.217813e+000.00e+00 3.370617e+000.00e+00 3.523421e+000.00e+00 3.676225e+000.00e+00 3.829029e+000.00e+00 3.981833e+000.00e+00 4.134637e+000.00e+00 4.287441e+000.00e+00 4.440246e+000.00e+00 4.593050e+000.00e+00 4.745854e+000.00e+00 4.898658e+000.00e+00 5.051462e+000.00e+00 5.204266e+000.00e+00 5.357070e+000.00e+00 5.509874e+000.00e+00 5.662678e+000.00e+00 5.815483e+000.00e+00 5.968287e+000.00e+00 The value of PMF is coming zero kCa/mol If i neglect the 6 windows before the last window then the pmf values are not zero. The obtained pmf curve is attached to the below link. https://www.dropbox.com/s/8tunpvfmnakupiu/pmf.jpg?dl=0 What may be reason could be? Can you please explain me. And please suggest me how to solve this problem. Thanks sathish On Mon, Oct 13, 2014 at 10:08 AM, Sathish Kumar sathishk...@gmail.com wrote: I am not able to find wheather the windows are overlaped or not. Please help me in this. Thanks. On Mon, Oct 13, 2014 at 10:05 AM, Sathish Kumar sathishk...@gmail.com wrote: Hai Yes, I have ploted the histogram, all windows are merged..please check this histo.jpg file attached to the below link. https://www.dropbox.com/s/ndl0w250dnawmib/histogram.jpg?dl=0 On Mon, Oct 13, 2014 at 3:47 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Does that mean the umbrella don't overlap enough at those z ? Can you make an overlay plot of the histograms of each umbrella? On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com wrote: Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Using g_wham, i got the profile.xvg, in that profile.xvg, all PMF values are zero. while running g_wham i am getting warings like below. WARNING, no data point in bin 163 (z=8.27767) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 164 (z=8.31563) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 165 (z=8.35358) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 194 (z=9.45432). Check your histograms! Initialized rapid wham stuff (contrib tolerance 1.31579e-08) Evaluating only 2619 of 15200 expressions. 1) Maximum change 3.178184e+02 100) Maximum change 1.611126e+00 200) Maximum change 3.303540e+00 300) Maximum change 1.239682e+00 400) Maximum change 1.383353e+00 500) Maximum change 1.116406e+00 600) Maximum change 1.241516e+00 700) Maximum change 1.028108e+00 800) Maximum change 1.698508e+00 900) Maximum change 1.331078e+00 Switched to exact iteration in iteration 983 Converged in 984 iterations. Final maximum change 0 Please help me in this regard. Thanks sathish -- 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. -- regards M.SathishKumar -- regards M.SathishKumar -- regards M.SathishKumar -- 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] Regarding umbrella samplling
Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Using g_wham, i got the profile.xvg, in that profile.xvg, all PMF values are zero. while running g_wham i am getting warings like below. WARNING, no data point in bin 163 (z=8.27767) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 164 (z=8.31563) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 165 (z=8.35358) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 194 (z=9.45432). Check your histograms! Initialized rapid wham stuff (contrib tolerance 1.31579e-08) Evaluating only 2619 of 15200 expressions. 1) Maximum change 3.178184e+02 100) Maximum change 1.611126e+00 200) Maximum change 3.303540e+00 300) Maximum change 1.239682e+00 400) Maximum change 1.383353e+00 500) Maximum change 1.116406e+00 600) Maximum change 1.241516e+00 700) Maximum change 1.028108e+00 800) Maximum change 1.698508e+00 900) Maximum change 1.331078e+00 Switched to exact iteration in iteration 983 Converged in 984 iterations. Final maximum change 0 Please help me in this regard. Thanks sathish -- 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] Regarding Umbrella samplling
On 9/29/14 10:09 AM, Sathish Kumar wrote: Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justinIn my system rna is binding with gold nanoparticle...to find out the binding energy i run the umbrella sampling using the space 0.2 nm and i got total 59 configurations, each configuration was run for 5 ns. The profile files are shared with the link below. https://www.dropbox.com/s/c8tj2rhu620xkim/Slide1.JPG?dl=0 https://www.dropbox.com/s/745kixwrfvguyyt/Slide2.JPG?dl=0 In the profile image, i have not got the plateu value, can i take the difference between final and starting pmf values for the binding enrgy. Please give suggestions. You don't have either a plateau or a defined minimum, so I'd say that the reaction coordinate is incomplete, either in terms of the sampling within the windows or the window setup itself. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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.
