Re: [gmx-users] PMF curve in umbrella sampling
On 8/30/14, 8:09 AM, Mana Ib wrote: Thankyou for your response. I spaced them at approx 0.05nm because at the 473rd configuration my ligand becomes solvated...and completely dissociated from the protein and there is a jump in the COM distances. Would you recommend running windows for configurations beyond 473 to get an accurate PMF curve? COM distances: 01.2500689 11.2390118 21.2656376 31.2382807 41.2464908 51.2613748 61.2571518 71.2494564 81.2383828 91.2645215 101.2555224 111.2915937 121.2589550 131.2495953 141.2489617 151.2657266 161.2611536 171.2734816 181.2627461 191.2537713 201.2643420 211.2796929 221.2557689 231.2522986 241.2710813 251.2805812 261.2488314 271.2324920 281.2218119 291.2351364 301.254 311.2607237 321.2823184 331.2744044 341.2816412 351.2946619 361.2658573 371.2778631 381.2684767 391.2577963 401.2658514 411.2675236 421.2645024 431.2517917 441.2668618 451.2837279 461.2711920 471.2984477 481.2850081 491.2738078 501.2791895 511.2671049 521.2689266 531.2527233 541.2541883 551.2683328 561.2879772 571.2765738 581.2745949 591.2624943 601.2713360 611.2903701 621.2538780 631.2524761 641.2804133 651.2904843 661.2767571 671.2811158 681.2873763 691.2897247 701.2967854 711.2898058 721.2866045 731.2680842 741.2828430 751.2517999 761.2789755 771.2674298 781.2963352 791.2863842 801.2686276 811.2527305 821.2675610 831.2817050 841.2519698 851.2547150 861.2316085 871.2301512 881.2587688 891.2676184 901.2682347 911.2762364 921.2774154 931.2711686 941.2815300 951.3117696 961.3037083 971.2877588 981.3003120 991.2830641 1001.2736199 1011.2975351 1021.2716285 1031.2636745 1041.2595536 1051.2820042 1061.2727789 1071.2464533 1081.2609475 1091.2909839 1101.2857704 1111.2857469 1121.2838980 1131.2866713 1141.2899315 1151.2773947 1161.2701035 1171.2897719 1181.2819400 1191.3044168 1201.2997466 1211.2958813 1221.2790420 1231.2786862 1241.2843164 1251.3100673 1261.2898589 1271.2878088 1281.2788408 1291.2817291 1301.2892330 1311.2841049 1321.2907283 1331.2960732 1341.2822367 1351.3024569 1361.2965143 1371.2839130 1381.2765539 1391.2846087 1401.2716116 1411.2829932 1421.2692751 1431.3112148 1441.3305217 1451.3154910 1461.2995077 1471.2961320 1481.3201323 1491.3076353 1501.3050537 1511.3059070 1521.3154420 1531.2943887 1541.3121384 1551.3134962 1561.3178825 1571.3217572 1581.2944893 1591.2979667 1601.2917393 1611.2989479 1621.3068420 1631.3138773 1641.2800533 1651.2904462 1661.2946355 1671.2841026 1681.2830913 1691.2916815 1701.3171769 1711.2839959 1721.2902473 1731.3021219 1741.3086892 1751.3062795 1761.2896782 1771.2646221 1781.2967244 1791.3318710 1801.3260037 1811.3066446 1821.3087828 1831.3031635 1841.2651044 1851.3077284 1861.2997077 1871.2937896 1881.3135617 1891.3186882 1901.3199843 1911.3641998 1921.3608552 1931.3191408 1941.3369676 1951.3495121 1961.3608030 1971.3640209 1981.3769726 1991.3143706 2001.3277380 2011.3327760 2021.3275329 2031.3249296 2041.3207476 2051.3446074 2061.3251934 2071.3521178 2081.3415477 2091.3205338 2101.3183049 2111.3279040 2121.3370273 2131.3558873 2141.3275462 2151.3397077 2161.3265324 2171.3250760 2181.3557339 2191.3370665 2201.3299704 2211.3431152 2221.3304195 2231.3742563 2241.3224043 2251.3176907 2261.3264394 2271.3246692 2281.3441764 2291.3347285 2301.3389533 2311.3308688 2321.3257663 2331.3243916 2341.3384953 2351.3148066 2361.2998172 2371.3078777 2381.3343482 2391.3064271 2401.3530262 2411.3190423 2421.3246952 2431.3256948 2441.3378791 2451.3348513 2461.3224670 2471.3466573 2481.3461218 2491.3204277 2501.3261340 2511.3477811 2521.3435458 2531.3670396 2541.3363574 2551.3268965 2561.3046312 2571.3266972 2581.3626263 2591.3708274 2601.3452878 2611.3339913 2621.3417501 2631.3323883 2641.3441674 2651.3532716 2661.3320799 2671.3409791 2681.3437917 2691.3395978 2701.3411486 2711.3256128 2721.3365294 2731.3508692 2741.3467736 2751.3287274 2761.3815287 2771.3535491 2781.3791600 279
Re: [gmx-users] PMF curve in umbrella sampling
Thankyou for your response. I spaced them at approx 0.05nm because at the 473rd configuration my ligand becomes solvated...and completely dissociated from the protein and there is a jump in the COM distances. Would you recommend running windows for configurations beyond 473 to get an accurate PMF curve? COM distances: 01.2500689 11.2390118 21.2656376 31.2382807 41.2464908 51.2613748 61.2571518 71.2494564 81.2383828 91.2645215 101.2555224 111.2915937 121.2589550 131.2495953 141.2489617 151.2657266 161.2611536 171.2734816 181.2627461 191.2537713 201.2643420 211.2796929 221.2557689 231.2522986 241.2710813 251.2805812 261.2488314 271.2324920 281.2218119 291.2351364 301.254 311.2607237 321.2823184 331.2744044 341.2816412 351.2946619 361.2658573 371.2778631 381.2684767 391.2577963 401.2658514 411.2675236 421.2645024 431.2517917 441.2668618 451.2837279 461.2711920 471.2984477 481.2850081 491.2738078 501.2791895 511.2671049 521.2689266 531.2527233 541.2541883 551.2683328 561.2879772 571.2765738 581.2745949 591.2624943 601.2713360 611.2903701 621.2538780 631.2524761 641.2804133 651.2904843 661.2767571 671.2811158 681.2873763 691.2897247 701.2967854 711.2898058 721.2866045 731.2680842 741.2828430 751.2517999 761.2789755 771.2674298 781.2963352 791.2863842 801.2686276 811.2527305 821.2675610 831.2817050 841.2519698 851.2547150 861.2316085 871.2301512 881.2587688 891.2676184 901.2682347 911.2762364 921.2774154 931.2711686 941.2815300 951.3117696 961.3037083 971.2877588 981.3003120 991.2830641 1001.2736199 1011.2975351 1021.2716285 1031.2636745 1041.2595536 1051.2820042 1061.2727789 1071.2464533 1081.2609475 1091.2909839 1101.2857704 1111.2857469 1121.2838980 1131.2866713 1141.2899315 1151.2773947 1161.2701035 1171.2897719 1181.2819400 1191.3044168 1201.2997466 1211.2958813 1221.2790420 1231.2786862 1241.2843164 1251.3100673 1261.2898589 1271.2878088 1281.2788408 1291.2817291 1301.2892330 1311.2841049 1321.2907283 1331.2960732 1341.2822367 1351.3024569 1361.2965143 1371.2839130 1381.2765539 1391.2846087 1401.2716116 1411.2829932 1421.2692751 1431.3112148 1441.3305217 1451.3154910 1461.2995077 1471.2961320 1481.3201323 1491.3076353 1501.3050537 1511.3059070 1521.3154420 1531.2943887 1541.3121384 1551.3134962 1561.3178825 1571.3217572 1581.2944893 1591.2979667 1601.2917393 1611.2989479 1621.3068420 1631.3138773 1641.2800533 1651.2904462 1661.2946355 1671.2841026 1681.2830913 1691.2916815 1701.3171769 1711.2839959 1721.2902473 1731.3021219 1741.3086892 1751.3062795 1761.2896782 1771.2646221 1781.2967244 1791.3318710 1801.3260037 1811.3066446 1821.3087828 1831.3031635 1841.2651044 1851.3077284 1861.2997077 1871.2937896 1881.3135617 1891.3186882 1901.3199843 1911.3641998 1921.3608552 1931.3191408 1941.3369676 1951.3495121 1961.3608030 1971.3640209 1981.3769726 1991.3143706 2001.3277380 2011.3327760 2021.3275329 2031.3249296 2041.3207476 2051.3446074 2061.3251934 2071.3521178 2081.3415477 2091.3205338 2101.3183049 2111.3279040 2121.3370273 2131.3558873 2141.3275462 2151.3397077 2161.3265324 2171.3250760 2181.3557339 2191.3370665 2201.3299704 2211.3431152 2221.3304195 2231.3742563 2241.3224043 2251.3176907 2261.3264394 2271.3246692 2281.3441764 2291.3347285 2301.3389533 2311.3308688 2321.3257663 2331.3243916 2341.3384953 2351.3148066 2361.2998172 2371.3078777 2381.3343482 2391.3064271 2401.3530262 2411.3190423 2421.3246952 2431.3256948 2441.3378791 2451.3348513 2461.3224670 2471.3466573 2481.3461218 2491.3204277 2501.3261340 2511.3477811 2521.3435458 2531.3670396 2541.3363574 2551.3268965 2561.3046312 2571.3266972 2581.3626263 2591.3708274 2601.3452878 2611.3339913 2621.3417501 2631.3323883 2641.3441674 2651.3532716 2661.3320799 2671.3409791 2681.3437917 2691.3395978 2701.3411486 2711.3256128 2721.3365294 2731.3508692 2741.3467736 2751.3287274 2761.3815287 2771.3535491 2781.3791600 2791.3642347 2801.3533387 281
[gmx-users] PMF curve in umbrella sampling
Dear Users, I am doing an umbrella sampling for a protein-ligand complex, wherein I first did an SMD run for 500 ps and generated 500 configurations, the COM distances for these configurations start at 1.25nm for conf0 and so on till 6.4nm for conf500. Hence I used a 0.05nm spacing to select configurations for the umbrella sampling windows. I have currently completed running 2 windows, each window was subjected to a 5ns mdrun. This is my mdp file parameters title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns nstcomm = 10 ; Output parameters nstxout = 5 ; every 100 ps nstvout = 5 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = NL pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 500 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps When I use g_wham to plot the histogram and PMF curve for these 2 windows, my plots don't seem to follow the general trend as given in tutorials..(figure links below). Is this discrepancy because I have used only files from 2 windows to plot these? Or are these due to some other errors in the protocol? http://i46.photobucket.com/albums/f121/fullmeasure29/histo_2win_zpsff19fe60.png http://i46.photobucket.com/albums/f121/fullmeasure29/pmf_2win_zps04adb8f7.png -- 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] PMF curve in umbrella sampling
On 8/29/14, 2:08 PM, Mana Ib wrote: Dear Users, I am doing an umbrella sampling for a protein-ligand complex, wherein I first did an SMD run for 500 ps and generated 500 configurations, the COM distances for these configurations start at 1.25nm for conf0 and so on till 6.4nm for conf500. Hence I used a 0.05nm spacing to select configurations for the umbrella sampling windows. I have currently completed running 2 windows, each window was subjected to a 5ns mdrun. This is my mdp file parameters title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns nstcomm = 10 ; Output parameters nstxout = 5 ; every 100 ps nstvout = 5 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 1 pull_group0 = Chain_A pull_group1 = NL pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 500 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps When I use g_wham to plot the histogram and PMF curve for these 2 windows, my plots don't seem to follow the general trend as given in tutorials..(figure links below). Is this discrepancy because I have used only files from 2 windows to plot these? Or are these due to some other errors in the protocol? http://i46.photobucket.com/albums/f121/fullmeasure29/histo_2win_zpsff19fe60.png http://i46.photobucket.com/albums/f121/fullmeasure29/pmf_2win_zps04adb8f7.png The two windows yield effectively overlapping distributions and a meaningless PMF. Space the windows further (0.05 nm is very tight) and run more windows for a real PMF as a function of a meaningful reaction coordinate. -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.
