how to run gromacs for protein protein interaction having phosphorylated at SER and THR. error: residue TPO not found in residue topology database modification are done from the given web. http://www.gromacs.org/Downloads/User_contributions/Force_fields
>make changes in .rtp file make changes in .dat file forcefield 43A1 is used. command: pdb2gmx -f protein.pdb -p protein.top -o protein.gro error: residue "TPO" not found in residue topology database make changes in residuestypes.dat fallowing are the changes make in .rtp file ; [ SEP ] [ TPO ] [ PTR ] -PO4^{-2} forms ; [ SEPH ] [ TPOH ] [ PTRH ] -PO4H^{-1} forms [ SEP ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 2 OG OA -0.36000 2 P P 0.94000 2 O1P OP -0.86000 2 O2P OP -0.86000 2 O3P OP -0.86000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG gb_17 OG P gb_27 P O1P gb_23 P O2P gb_23 P O3P gb_23 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG ga_12 CB OG P ga_25 OG P O1P ga_13 OG P O2P ga_13 OG P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG gd_17 CA CB OG P gd_14 CB OG P O1P gd_11 [ TPO ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.00000 2 OG1 OA -0.36000 2 P P 0.94000 2 O1P OP -0.86000 2 O2P OP -0.86000 2 O3P OP -0.86000 2 CG2 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 P gb_27 P O1P gb_23 P O2P gb_23 P O3P gb_23 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_14 OG1 CB CG2 ga_14 CB OG1 P ga_25 OG1 P O1P ga_13 OG1 P O2P ga_13 OG1 P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG1 gd_17 CA CB OG1 P gd_14 CB OG1 P O1P gd_11 [ PTR ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C -0.10000 4 HE1 HC 0.10000 4 CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ C 0.00000 6 OH OA -0.36000 6 P P 0.94000 6 O1P OP -0.86000 6 O2P OP -0.86000 6 O3P OP -0.86000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 HE1 gb_3 CE1 CZ gb_15 CE2 HE2 gb_3 CE2 CZ gb_15 CZ OH gb_12 OH P gb_27 P O1P gb_23 P O2P gb_23 P O3P gb_23 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE1 CG HE2 CG CZ CD1 HD2 CD1 CE2 CD1 OH HD1 CD2 HD1 HE1 HD1 CZ CD2 CE1 CD2 OH HD2 HE2 HD2 CZ CE1 HE2 HE1 CE2 HE1 OH HE2 OH [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 HE1 ga_24 HE1 CE1 CZ ga_24 CD1 CE1 CZ ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ ga_24 CD2 CE2 CZ ga_26 CE1 CZ CE2 ga_26 CE1 CZ OH ga_26 CE2 CZ OH ga_26 CZ OH P ga_25 OH P O1P ga_13 OH P O2P ga_13 OH P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 CD1 CE1 CZ CE2 gi_1 CD2 CE2 CZ CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ CD1 HE1 gi_1 CE2 CZ CD2 HE2 gi_1 CZ CE1 CE2 OH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ OH P gd_14 CZ OH P O1P gd_11 ; end [ SEPH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 2 OG OA -0.36000 2 P P 1.23000 2 O1P OP -0.86000 2 O2P OP -0.86000 2 O3P OA -0.54800 2 H3P H 0.39800 2 C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG gb_17 OG P gb_27 P O1P gb_23 P O2P gb_23 P O3P gb_23 O3P H3P gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG ga_12 CB OG P ga_25 OG P O1P ga_13 OG P O2P ga_13 OG P O3P ga_4 O1P P O2P ga_28 O1P P O3P ga_13 O2P P O3P ga_13 P O3P H3P ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG gd_17 CA CB OG P gd_14 CB OG P O1P gd_11 OG P O3P H3P gd_11 [ TPOH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.00000 2 OG1 OA -0.36000 2 P P 1.23000 2 O1P OP -0.86000 2 O2P OP -0.86000 2 O3P OA -0.54800 2 H3P H 0.39800 2 CG2 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 P gb_27 P O1P gb_23 P O2P gb_23 P O3P gb_23 O3P H3P gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_14 OG1 CB CG2 ga_14 CB OG1 P ga_25 OG1 P O1P ga_13 OG1 P O2P ga_13 OG1 P O3P ga_4 O1P P O2P ga_28 O1P P O3P ga_13 O2P P O3P ga_13 P O3P H3P ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG1 gd_17 CA CB OG1 P gd_14 CB OG1 P O1P gd_11 OG1 P O3P H3P gd_11 [ PTRH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C -0.10000 4 HE1 HC 0.10000 4 CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ C 0.00000 6 OH OA -0.36000 6 P P 1.23000 6 O1P OP -0.86000 6 O2P OP -0.86000 6 O3P OA -0.54800 6 H3P H 0.39800 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 HE1 gb_3 CE1 CZ gb_15 CE2 HE2 gb_3 CE2 CZ gb_15 CZ OH gb_12 OH P gb_27 P O1P gb_23 P O2P gb_23 P O3P gb_23 O3P H3P gb_1 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE1 CG HE2 CG CZ CD1 HD2 CD1 CE2 CD1 OH HD1 CD2 HD1 HE1 HD1 CZ CD2 CE1 CD2 OH HD2 HE2 HD2 CZ CE1 HE2 HE1 CE2 HE1 OH HE2 OH [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 HE1 ga_24 HE1 CE1 CZ ga_24 CD1 CE1 CZ ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ ga_24 CD2 CE2 CZ ga_26 CE1 CZ CE2 ga_26 CE1 CZ OH ga_26 CE2 CZ OH ga_26 CZ OH P ga_25 OH P O1P ga_13 OH P O2P ga_13 OH P O3P ga_4 O1P P O2P ga_13 O1P P O3P ga_13 O2P P O3P ga_28 P O3P H3P ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 CD1 CE1 CZ CE2 gi_1 CD2 CE2 CZ CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ CD1 HE1 gi_1 CE2 CZ CD2 HE2 gi_1 CZ CE1 CE2 OH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ OH P gd_14 CZ OH P O1P gd_11 OH P O3P H3P gd_11 ; end insert from pamac_hsn.rtp -------------------------------------------- On Mon, 1/2/16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se <gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 1 To: gromacs.org_gmx-users@maillist.sys.kth.se Received: Monday, 1 February, 2016, 9:50 AM Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. relative binding free energy calculation Gromacs 5.0.5 (Stefania Evoli) 2. Re: relative binding free energy calculation Gromacs 5.0.5 (hannes.loeff...@stfc.ac.uk) 3. gmx sasa (Eric Smoll) 4. Re: gmx sasa (Justin Lemkul) 5. g_count (vgsplayer1) 6. Re: g_count (Mark Abraham) ---------------------------------------------------------------------- Message: 1 Date: Sun, 31 Jan 2016 12:59:10 +0000 From: Stefania Evoli <stefania.ev...@kaust.edu.sa> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> Subject: [gmx-users] relative binding free energy calculation Gromacs 5.0.5 Message-ID: <d2d3dfc6.41f4%stefania.ev...@kaust.edu.sa> Content-Type: text/plain; charset="Windows-1252" Dear users, I?m performing relative binding free energy calculation in Gromacs 5.0.5. In the mdp files I?m using the following section free-energy = yes init_lambda_state = LAMBDA fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw_lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 ;couple-moltype = LIG ;couple-lambda0 = vdw-q ;couple-lambda1 = none ;couple-intramol = no sc-alpha = 0.5 sc-sigma = 0.3 sc-power = 1.0 sc-r-power = 6 sc-coul = no nstdhdl = 100 calc-lambda-neighbors = -1 And I obtained the following values 0 -- 1 16.498 +- 0.147 16.458 +- 0.173 18.142 +- 0.465 13.644 +- 0.351 16.264 +- 0.411 16.264 +- 0.413 1 -- 2 7.086 +- 0.143 6.982 +- 0.159 10.223 +- 0.246 4.168 +- 0.299 6.971 +- 0.341 6.971 +- 0.454 2 -- 3 -1.954 +- 0.114 -1.685 +- 0.129 -1.043 +- 0.574 -3.884 +- 0.392 -1.883 +- 0.356 -1.883 +- 0.356 3 -- 4 -13.604 +- 0.139 -13.271 +- 0.145 -10.960 +- 0.574 -18.048 +- 0.234 -14.286 +- 0.601 -13.222 +- 0.167 4 -- 5 0.089 +- 0.003 0.093 +- 0.003 0.079 +- 0.005 0.099 +- 0.003 0.091 +- 0.003 0.085 +- 0.000 5 -- 6 0.078 +- 0.004 0.079 +- 0.004 0.094 +- 0.003 0.062 +- 0.008 0.087 +- 0.003 0.080 +- 0.000 6 -- 7 0.141 +- 0.008 0.130 +- 0.011 0.110 +- 0.017 0.170 +- 0.001 0.170 +- 0.001 0.143 +- 0.001 7 -- 8 0.123 +- 0.005 0.131 +- 0.006 0.155 +- 0.001 0.096 +- 0.011 0.154 +- 0.001 0.121 +- 0.001 8 -- 9 0.063 +- 0.005 0.063 +- 0.006 0.071 +- 0.011 0.056 +- 0.001 0.056 +- 0.001 0.095 +- 0.001 9 -- 10 0.012 +- 0.004 0.002 +- 0.005 0.028 +- 0.001 -0.004 +- 0.008 0.028 +- 0.001 0.065 +- 0.001 10 -- 11 0.019 +- 0.008 0.030 +- 0.011 -0.036 +- 0.009 0.084 +- 0.011 0.007 +- 0.007 0.027 +- 0.001 11 -- 12 0.016 +- 0.006 0.013 +- 0.007 0.019 +- 0.008 0.008 +- 0.009 0.018 +- 0.006 -0.004 +- 0.000 12 -- 13 0.012 +- 0.007 0.015 +- 0.008 -0.004 +- 0.010 0.028 +- 0.009 0.012 +- 0.007 -0.018 +- 0.000 13 -- 14 -0.011 +- 0.008 -0.010 +- 0.009 0.015 +- 0.011 -0.034 +- 0.010 -0.011 +- 0.008 -0.034 +- 0.000 14 -- 15 -0.049 +- 0.006 -0.049 +- 0.007 -0.055 +- 0.014 -0.044 +- 0.001 -0.044 +- 0.001 -0.054 +- 0.000 15 -- 16 -0.085 +- 0.003 -0.086 +- 0.004 -0.065 +- 0.001 -0.104 +- 0.005 -0.066 +- 0.001 -0.078 +- 0.001 16 -- 17 -0.116 +- 0.009 -0.116 +- 0.010 -0.132 +- 0.006 -0.100 +- 0.016 -0.129 +- 0.006 -0.109 +- 0.001 17 -- 18 -0.150 +- 0.009 -0.145 +- 0.010 -0.129 +- 0.018 -0.159 +- 0.001 -0.159 +- 0.001 -0.151 +- 0.001 18 -- 19 -0.218 +- 0.005 -0.220 +- 0.005 -0.219 +- 0.002 -0.218 +- 0.008 -0.219 +- 0.002 -0.211 +- 0.001 It is clear the instability of the first four lambda values. Can someone suggest me a way to avoid it? I?m trying to use different sc-alpha, sc-power and sc-r-power. Any suggestion? Thank you, Stefania ? Dr. Stefania Evoli Post-Doctoral Fellow King Abdullah University of Science and Technology Catalysis center - Bldg. 3, 4th floor, 4231?WS18 Thuwal, Kingdom of Saudi Arabia stefania.ev...@kaust.edu.sa ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ------------------------------ Message: 2 Date: Sun, 31 Jan 2016 15:13:36 +0000 From: <hannes.loeff...@stfc.ac.uk> To: <gmx-us...@gromacs.org> Subject: Re: [gmx-users] relative binding free energy calculation Gromacs 5.0.5 Message-ID: <5ff52965bbb9cb46930c7e5d323ec021e6c99...@exchmbx01.fed.cclrc.ac.uk> Content-Type: text/plain; charset="Windows-1252" What do you mean by "instability"? You also don't quite say what these values mean but I guess they are the estimates of the free energy per each window as computed by different methods(?). These values come obviously from the (linear) electrostatic transformation so playing with softcore parameters won't make any difference. If you are concerned by their magnitudes you can always introduce additional lambda points. BTW, you may want to keep the mass-lambdas at their initial values (see mailing list archive for details). ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Stefania Evoli [stefania.ev...@kaust.edu.sa] Sent: 31 January 2016 12:59 To: gmx-us...@gromacs.org Subject: [gmx-users] relative binding free energy calculation Gromacs 5.0.5 Dear users, I?m performing relative binding free energy calculation in Gromacs 5.0.5. In the mdp files I?m using the following section free-energy = yes init_lambda_state = LAMBDA fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw_lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 ;couple-moltype = LIG ;couple-lambda0 = vdw-q ;couple-lambda1 = none ;couple-intramol = no sc-alpha = 0.5 sc-sigma = 0.3 sc-power = 1.0 sc-r-power = 6 sc-coul = no nstdhdl = 100 calc-lambda-neighbors = -1 And I obtained the following values 0 -- 1 16.498 +- 0.147 16.458 +- 0.173 18.142 +- 0.465 13.644 +- 0.351 16.264 +- 0.411 16.264 +- 0.413 1 -- 2 7.086 +- 0.143 6.982 +- 0.159 10.223 +- 0.246 4.168 +- 0.299 6.971 +- 0.341 6.971 +- 0.454 2 -- 3 -1.954 +- 0.114 -1.685 +- 0.129 -1.043 +- 0.574 -3.884 +- 0.392 -1.883 +- 0.356 -1.883 +- 0.356 3 -- 4 -13.604 +- 0.139 -13.271 +- 0.145 -10.960 +- 0.574 -18.048 +- 0.234 -14.286 +- 0.601 -13.222 +- 0.167 4 -- 5 0.089 +- 0.003 0.093 +- 0.003 0.079 +- 0.005 0.099 +- 0.003 0.091 +- 0.003 0.085 +- 0.000 5 -- 6 0.078 +- 0.004 0.079 +- 0.004 0.094 +- 0.003 0.062 +- 0.008 0.087 +- 0.003 0.080 +- 0.000 6 -- 7 0.141 +- 0.008 0.130 +- 0.011 0.110 +- 0.017 0.170 +- 0.001 0.170 +- 0.001 0.143 +- 0.001 7 -- 8 0.123 +- 0.005 0.131 +- 0.006 0.155 +- 0.001 0.096 +- 0.011 0.154 +- 0.001 0.121 +- 0.001 8 -- 9 0.063 +- 0.005 0.063 +- 0.006 0.071 +- 0.011 0.056 +- 0.001 0.056 +- 0.001 0.095 +- 0.001 9 -- 10 0.012 +- 0.004 0.002 +- 0.005 0.028 +- 0.001 -0.004 +- 0.008 0.028 +- 0.001 0.065 +- 0.001 10 -- 11 0.019 +- 0.008 0.030 +- 0.011 -0.036 +- 0.009 0.084 +- 0.011 0.007 +- 0.007 0.027 +- 0.001 11 -- 12 0.016 +- 0.006 0.013 +- 0.007 0.019 +- 0.008 0.008 +- 0.009 0.018 +- 0.006 -0.004 +- 0.000 12 -- 13 0.012 +- 0.007 0.015 +- 0.008 -0.004 +- 0.010 0.028 +- 0.009 0.012 +- 0.007 -0.018 +- 0.000 13 -- 14 -0.011 +- 0.008 -0.010 +- 0.009 0.015 +- 0.011 -0.034 +- 0.010 -0.011 +- 0.008 -0.034 +- 0.000 14 -- 15 -0.049 +- 0.006 -0.049 +- 0.007 -0.055 +- 0.014 -0.044 +- 0.001 -0.044 +- 0.001 -0.054 +- 0.000 15 -- 16 -0.085 +- 0.003 -0.086 +- 0.004 -0.065 +- 0.001 -0.104 +- 0.005 -0.066 +- 0.001 -0.078 +- 0.001 16 -- 17 -0.116 +- 0.009 -0.116 +- 0.010 -0.132 +- 0.006 -0.100 +- 0.016 -0.129 +- 0.006 -0.109 +- 0.001 17 -- 18 -0.150 +- 0.009 -0.145 +- 0.010 -0.129 +- 0.018 -0.159 +- 0.001 -0.159 +- 0.001 -0.151 +- 0.001 18 -- 19 -0.218 +- 0.005 -0.220 +- 0.005 -0.219 +- 0.002 -0.218 +- 0.008 -0.219 +- 0.002 -0.211 +- 0.001 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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