Thanks Justin, I am not setting any Lennard-Jones parameters to zero for part B. I put zero charge on all atoms for Part B. (Lennard Jones parameters for B are same as Part A).
I am using default parameters for "couple-lambda0" and "couple-lambda1". For one of my simulation (glucose + ionic liquids) I am getting solvation free energy 35.5 Kcal/mol. Is it too high? Nilesh On Sun, January 10, 2010 1:08 pm, Justin A. Lemkul wrote: > > > On 1/10/10 1:03 PM, Nilesh Dhumal wrote: > >> Hello Justin, >> Should I add dum_opls no. in atom type file in which Lennard-jones >> parameters will set to zero. OR. >> I don't have to modify anything prog.will take care of lennard-jones >> interactions. I have put charge zero on all atom in TYPE B. >> > > You shouldn't have to do make any modifications to the topology > whatsoever, according to the documentation. The "couple-lambda0" and > "couple-lambda1" > parameters should do the decoupling for you. > > -Justin > > >> Nilesh >> >> >> On Sun, January 3, 2010 12:57 pm, Justin A. Lemkul wrote: >> >>> >> >>> >>> Nilesh Dhumal wrote: >>> >>> >>>> THanks Justin. >>>> I am using Groamcs 4.0.7 version. I will do more simulation with >>>> more lambada value betwen 0 to 0.1. >>> >>> I really think this is less significant than point #1 I mentioned >>> before. Be >>> sure you are actually setting the relevant .mdp parameters >>> (couple-lambda0, >>> couple-lambda1, etc) as they will heavily influence the results. >>> Leaving >>> them as default (as you are doing, per the .mdp file you provided) may >>> give you something other than what you want. >>> >>> And do consult the links I provided; they give excellent background >>> on the nature of these calculations. >>> >>> -Justin >>> >>> >>> >>>> Thanks. >>>> Nilesh >>>> >>>> >>>> >>>> On Sun, January 3, 2010 12:39 pm, Justin A. Lemkul wrote: >>>> >>>> >>>> >>>>> Nilesh Dhumal wrote: >>>>> >>>>> >>>>> >>>>>> Hey All, >>>>>> I am trying to calculate the solvation free energy of glucose in >>>>>> ionic liquids. I am getting really large value for lamda=0 in >>>>>> vacuum and solvent as well. I am getting final solvation >>>>>> energy value ~ 310 kJ/mol. Can you tell me where I am wrong. >>>>>> >>>>> There are several possibilities: >>>>> >>>>> >>>>> >>>>> >>>>> 1. Are you decoupling LJ and Coulombic interactions >>>>> simultaneously? They >>>>> should be done in separate steps, or else you get very large >>>>> errors. >>>>> >>>>> 2. You probably need a lot more lambda points to properly define >>>>> the curve. For strongly hydrogen-bonding solutes, you should >>>>> probably include closely-spaced points near lambda = 0 (the >>>>> fully-coupled state), like 0.005, 0.01, 0.015, etc. The curve from >>>>> 0 to 0.1 will otherwise be ill-defined and prone to large errors. >>>>> >>>>> You also do not say which version of the code you are using. The >>>>> free energy code has been tweaked in version 4.0 such that >>>>> topology handling is different, and the procedure is actually >>>>> quite a bit more streamlined, given the .mdp options. >>>>> >>>>> Might I recommend: >>>>> >>>>> >>>>> >>>>> >>>>> http://www.alchemistry.org/wiki/index.php/Best_Practices >>>>> >>>>> >>>>> >>>>> >>>>> http://md.chem.rug.nl/education/Free-Energy_Course/index.html >>>>> >>>>> >>>>> >>>>> >>>>> -Justin >>>>> >>>>> >>>>> >>>>> >>>>>> Here I have pasted the the lamda value in vacuum and solvent >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Vacuum Solvent >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 0.0 527.16 0.0 4284.769 >>>>>> 0.1 74.119 0.1 161.606 >>>>>> 0.2 37.9665 0.2 -16.3176 >>>>>> 0.3 28.748 0.3 -52.488 >>>>>> 0.4 7.555 0.4 -4.3341 >>>>>> 0.5 1.495 0.5 6.996 >>>>>> 0.6 -4.796 0.6 155.485 >>>>>> 0.7 2.361 0.7 174.20 >>>>>> 0.8 3.69 0.8 193.016 >>>>>> 0.9 5.483 0.9 201.820 >>>>>> 0.92 6.391 0.92 211.79 >>>>>> 1.0 8.887 1.0 227.79 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> For each lamda value I equibrate the system for 1ns and run the >>>>>> dynamics for 4 ns. here is dynamics file I used. pasted the >>>>>> topology file at the end. >>>>>> >>>>>> >>>>>> title = cpeptide MD cpp = >>>>>> /usr/bin/cpp >>>>>> constraints = none integrator = md dt = >>>>>> 0.001 >>>>>> ; ps ! >>>>>> nsteps = 4000000 ; total 5 ps. nstcomm = 1 >>>>>> nstxout = 50 nstvout = 0 nstfout = >>>>>> 0 >>>>>> nstlist = 10 ns_type = grid rlist = >>>>>> 1.0 >>>>>> rcoulomb = 1.0 rvdw = 1.4 >>>>>> coulombtype = PME >>>>>> vdwtype = cut-off pbc = xyz >>>>>> 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 >>>>>> Tcoupl = v-rescale tau_t = 0.1 tc-grps >>>>>> =system ref_t = 350 ; Pressure coupling is on >>>>>> Pcoupl = parrinello-rahman >>>>>> pcoupltype = isotropic tau_p = 0.5 >>>>>> compressibility = 4.5e-5 ref_p = 1.0 ; Generate >>>>>> velocites is on at 300 K. gen_vel = yes gen_temp >>>>>> = 350.0 gen_seed = >>>>>> 173529 >>>>>> free_energy = yes init_lambda = 0.00 sc-alpha = >>>>>> 0.6 >>>>>> sc_power = 1 >>>>>> >>>>>> >>>>>> Thanks >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Nilesh >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Topology file (not pasted whole because of size) >>>>>> ; >>>>>> ; File 'glu-ac.top' was generated >>>>>> ; By user: ndhumal (36026) >>>>>> ; On host: c20 >>>>>> ; At date: Tue Dec 15 15:25:07 2009 >>>>>> ; >>>>>> ; This is your topology file >>>>>> ; Gromacs Runs One Microsecond At Cannonball Speeds >>>>>> ; >>>>>> ; Include forcefield parameters >>>>>> #include "ffoplsaa.itp" >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> [ moleculetype ] >>>>>> ; Name nrexcl >>>>>> Protein 3 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> [ atoms ] >>>>>> ; nr type resnr residue atom cgnr charge >>>>>> mass typeB chargeB massB 1 opls_180 1 GUL O >>>>>> 1 >>>>>> -0.4 15.9994 >>>>>> opls_180 0.0 15.9994 2 opls_159 1 GUL C2 >>>>>> 2 >>>>>> 0.365 12.011 >>>>>> opls_159 0.0 12.011 3 opls_159 1 GUL C3 >>>>>> 2 >>>>>> 0.205 12.011 >>>>>> opls_159 0.0 12.011 4 opls_159 1 GUL C4 >>>>>> 2 >>>>>> 0.205 12.011 >>>>>> opls_159 0.0 12.011 5 opls_159 1 GUL C5 >>>>>> 2 >>>>>> 0.205 12.011 >>>>>> opls_159 0.0 12.011 6 opls_137 1 GUL C6 >>>>>> 2 >>>>>> 0.17 12.011 >>>>>> opls_137 0.0 12.011 7 opls_159 1 GUL C7 >>>>>> 2 >>>>>> 0.145 12.011 >>>>>> opls_159 0.0 12.011 8 opls_169 1 GUL O8 >>>>>> 3 >>>>>> -0.7 15.9994 >>>>>> opls_169 0.0 15.9994 9 opls_169 1 GUL O9 >>>>>> 3 >>>>>> -0.7 15.9994 >>>>>> opls_169 0.0 15.9994 10 opls_169 1 GUL O10 >>>>>> 3 >>>>>> -0.7 15.9994 >>>>>> opls_169 0.0 15.9994 11 opls_169 1 GUL O11 >>>>>> 3 >>>>>> -0.7 15.9994 >>>>>> opls_169 0.0 15.9994 12 opls_154 1 GUL O12 >>>>>> 3 >>>>>> -0.683 15.9994 >>>>>> opls_154 0.0 15.9994 13 opls_140 1 GUL H13 >>>>>> 4 >>>>>> 0.1 1.008 >>>>>> opls_140 0.0 1.008 14 opls_140 1 GUL H14 >>>>>> 4 >>>>>> 0.06 1.008 >>>>>> opls_140 0.0 1.008 15 opls_140 1 GUL H15 >>>>>> 4 >>>>>> 0.06 1.008 >>>>>> opls_140 0.0 1.008 16 opls_140 1 GUL H16 >>>>>> 4 >>>>>> 0.06 1.008 >>>>>> opls_140 0.0 1.008 17 opls_140 1 GUL H17 >>>>>> 4 >>>>>> 0.03 1.008 >>>>>> opls_140 0.0 1.008 18 opls_155 1 GUL H18 >>>>>> 5 >>>>>> 0.435 1.008 >>>>>> opls_155 0.0 1.008 19 opls_155 1 GUL H19 >>>>>> 5 >>>>>> 0.435 1.008 >>>>>> opls_155 0.0 1.008 20 opls_155 1 GUL H20 >>>>>> 5 >>>>>> 0.435 1.008 >>>>>> opls_155 0.0 1.008 21 opls_155 1 GUL H21 >>>>>> 5 >>>>>> 0.435 1.008 >>>>>> opls_155 0.0 1.008 22 opls_140 1 GUL H22 >>>>>> 5 >>>>>> 0.06 1.008 >>>>>> opls_140 0.0 1.008 23 opls_140 1 GUL H23 >>>>>> 5 >>>>>> 0.06 1.008 >>>>>> opls_140 0.0 1.008 24 opls_155 1 GUL H24 >>>>>> 6 >>>>>> 0.418 1.008 >>>>>> opls_155 0.0 1.008 25 opls_561 2 EMI C >>>>>> 7 >>>>>> -0.13 12.011 ; >>>>>> qtot -0.13 26 opls_561 2 EMI C2 8 -0.13 >>>>>> 12.011 ; >>>>>> qtot -0.26 27 opls_557 2 EMI N3 9 0.15 >>>>>> 14.0067 ; >>>>>> qtot -0.11 28 opls_558 2 EMI C4 10 -0.11 >>>>>> 12.011 ; >>>>>> qtot -0.22 29 opls_557 2 EMI N5 11 0.15 >>>>>> 14.0067 ; >>>>>> qtot -0.07 30 opls_135 2 EMI C6 12 -0.17 >>>>>> 12.011 ; >>>>>> qtot -0.24 31 opls_136 2 EMI C7 13 -0.05 >>>>>> 12.011 ; >>>>>> qtot -0.29 32 opls_135 2 EMI C8 14 -0.17 >>>>>> 12.011 ; >>>>>> qtot -0.46 33 opls_564 2 EMI H9 15 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot -0.25 34 opls_564 2 EMI H10 15 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot -0.04 35 opls_563 2 EMI H11 15 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.17 36 opls_140 2 EMI H12 16 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.3 37 opls_140 2 EMI H13 16 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.43 38 opls_140 2 EMI H14 16 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.56 39 opls_140 2 EMI H15 17 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.69 40 opls_140 2 EMI H16 17 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.82 41 opls_140 2 EMI H17 18 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.88 42 opls_140 2 EMI H18 18 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.94 43 opls_140 2 EMI H19 18 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1 44 opls_561 3 EMI C 19 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 0.87 45 opls_561 3 EMI C2 20 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 0.74 46 opls_557 3 EMI N3 21 0.15 >>>>>> 14.0067 >>>>>> ; >>>>>> qtot 0.89 47 opls_558 3 EMI C4 22 -0.11 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 0.78 48 opls_557 3 EMI N5 23 0.15 >>>>>> 14.0067 >>>>>> ; >>>>>> qtot 0.93 49 opls_135 3 EMI C6 24 -0.17 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 0.76 50 opls_136 3 EMI C7 25 -0.05 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 0.71 51 opls_135 3 EMI C8 26 -0.17 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 0.54 52 opls_564 3 EMI H9 27 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.75 53 opls_564 3 EMI H10 27 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 0.96 54 opls_563 3 EMI H11 27 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.17 55 opls_140 3 EMI H12 28 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.3 56 opls_140 3 EMI H13 28 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.43 57 opls_140 3 EMI H14 28 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.56 58 opls_140 3 EMI H15 29 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.69 59 opls_140 3 EMI H16 29 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.82 60 opls_140 3 EMI H17 30 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.88 61 opls_140 3 EMI H18 30 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.94 62 opls_140 3 EMI H19 30 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2 63 opls_561 4 EMI C 31 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 1.87 64 opls_561 4 EMI C2 32 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 1.74 65 opls_557 4 EMI N3 33 0.15 >>>>>> 14.0067 >>>>>> ; >>>>>> qtot 1.89 66 opls_558 4 EMI C4 34 -0.11 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 1.78 67 opls_557 4 EMI N5 35 0.15 >>>>>> 14.0067 >>>>>> ; >>>>>> qtot 1.93 68 opls_135 4 EMI C6 36 -0.17 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 1.76 69 opls_136 4 EMI C7 37 -0.05 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 1.71 70 opls_135 4 EMI C8 38 -0.17 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 1.54 71 opls_564 4 EMI H9 39 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.75 72 opls_564 4 EMI H10 39 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 1.96 73 opls_563 4 EMI H11 39 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.17 74 opls_140 4 EMI H12 40 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.3 75 opls_140 4 EMI H13 40 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.43 76 opls_140 4 EMI H14 40 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.56 77 opls_140 4 EMI H15 41 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.69 78 opls_140 4 EMI H16 41 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.82 79 opls_140 4 EMI H17 42 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.88 80 opls_140 4 EMI H18 42 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.94 81 opls_140 4 EMI H19 42 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3 82 opls_561 5 EMI C 43 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 2.87 83 opls_561 5 EMI C2 44 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 2.74 84 opls_557 5 EMI N3 45 0.15 >>>>>> 14.0067 >>>>>> ; >>>>>> qtot 2.89 85 opls_558 5 EMI C4 46 -0.11 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 2.78 86 opls_557 5 EMI N5 47 0.15 >>>>>> 14.0067 >>>>>> ; >>>>>> qtot 2.93 87 opls_135 5 EMI C6 48 -0.17 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 2.76 88 opls_136 5 EMI C7 49 -0.05 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 2.71 89 opls_135 5 EMI C8 50 -0.17 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 2.54 90 opls_564 5 EMI H9 51 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.75 91 opls_564 5 EMI H10 51 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 2.96 92 opls_563 5 EMI H11 51 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.17 93 opls_140 5 EMI H12 52 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.3 94 opls_140 5 EMI H13 52 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.43 95 opls_140 5 EMI H14 52 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.56 96 opls_140 5 EMI H15 53 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.69 97 opls_140 5 EMI H16 53 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.82 98 opls_140 5 EMI H17 54 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.88 99 opls_140 5 EMI H18 54 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.94 100 opls_140 5 EMI H19 54 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4 101 opls_561 6 EMI C 55 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 3.87 102 opls_561 6 EMI C2 56 -0.13 >>>>>> 12.011 ; >>>>>> qtot 3.74 103 opls_557 6 EMI N3 57 0.15 >>>>>> 14.0067 ; >>>>>> qtot 3.89 104 opls_558 6 EMI C4 58 -0.11 >>>>>> 12.011 ; >>>>>> qtot 3.78 105 opls_557 6 EMI N5 59 0.15 >>>>>> 14.0067 ; >>>>>> qtot 3.93 106 opls_135 6 EMI C6 60 -0.17 >>>>>> 12.011 ; >>>>>> qtot 3.76 107 opls_136 6 EMI C7 61 -0.05 >>>>>> 12.011 ; >>>>>> qtot 3.71 108 opls_135 6 EMI C8 62 -0.17 >>>>>> 12.011 ; >>>>>> qtot 3.54 109 opls_564 6 EMI H9 63 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.75 110 opls_564 6 EMI H10 63 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 3.96 111 opls_563 6 EMI H11 63 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.17 112 opls_140 6 EMI H12 64 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.3 113 opls_140 6 EMI H13 64 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.43 114 opls_140 6 EMI H14 64 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.56 115 opls_140 6 EMI H15 65 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.69 116 opls_140 6 EMI H16 65 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.82 117 opls_140 6 EMI H17 66 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.88 118 opls_140 6 EMI H18 66 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.94 119 opls_140 6 EMI H19 66 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5 120 opls_561 7 EMI C 67 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 4.87 121 opls_561 7 EMI C2 68 -0.13 >>>>>> 12.011 ; >>>>>> qtot 4.74 122 opls_557 7 EMI N3 69 0.15 >>>>>> 14.0067 ; >>>>>> qtot 4.89 123 opls_558 7 EMI C4 70 -0.11 >>>>>> 12.011 ; >>>>>> qtot 4.78 124 opls_557 7 EMI N5 71 0.15 >>>>>> 14.0067 ; >>>>>> qtot 4.93 125 opls_135 7 EMI C6 72 -0.17 >>>>>> 12.011 ; >>>>>> qtot 4.76 126 opls_136 7 EMI C7 73 -0.05 >>>>>> 12.011 ; >>>>>> qtot 4.71 127 opls_135 7 EMI C8 74 -0.17 >>>>>> 12.011 ; >>>>>> qtot 4.54 128 opls_564 7 EMI H9 75 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.75 129 opls_564 7 EMI H10 75 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 4.96 130 opls_563 7 EMI H11 75 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.17 131 opls_140 7 EMI H12 76 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.3 132 opls_140 7 EMI H13 76 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.43 133 opls_140 7 EMI H14 76 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.56 134 opls_140 7 EMI H15 77 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.69 135 opls_140 7 EMI H16 77 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.82 136 opls_140 7 EMI H17 78 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.88 137 opls_140 7 EMI H18 78 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.94 138 opls_140 7 EMI H19 78 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6 139 opls_561 8 EMI C 79 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 5.87 140 opls_561 8 EMI C2 80 -0.13 >>>>>> 12.011 ; >>>>>> qtot 5.74 141 opls_557 8 EMI N3 81 0.15 >>>>>> 14.0067 ; >>>>>> qtot 5.89 142 opls_558 8 EMI C4 82 -0.11 >>>>>> 12.011 ; >>>>>> qtot 5.78 143 opls_557 8 EMI N5 83 0.15 >>>>>> 14.0067 ; >>>>>> qtot 5.93 144 opls_135 8 EMI C6 84 -0.17 >>>>>> 12.011 ; >>>>>> qtot 5.76 145 opls_136 8 EMI C7 85 -0.05 >>>>>> 12.011 ; >>>>>> qtot 5.71 146 opls_135 8 EMI C8 86 -0.17 >>>>>> 12.011 ; >>>>>> qtot 5.54 147 opls_564 8 EMI H9 87 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.75 148 opls_564 8 EMI H10 87 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 5.96 149 opls_563 8 EMI H11 87 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.17 150 opls_140 8 EMI H12 88 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.3 151 opls_140 8 EMI H13 88 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.43 152 opls_140 8 EMI H14 88 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.56 153 opls_140 8 EMI H15 89 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.69 154 opls_140 8 EMI H16 89 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.82 155 opls_140 8 EMI H17 90 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.88 156 opls_140 8 EMI H18 90 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.94 157 opls_140 8 EMI H19 90 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7 158 opls_561 9 EMI C 91 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 6.87 159 opls_561 9 EMI C2 92 -0.13 >>>>>> 12.011 ; >>>>>> qtot 6.74 160 opls_557 9 EMI N3 93 0.15 >>>>>> 14.0067 ; >>>>>> qtot 6.89 161 opls_558 9 EMI C4 94 -0.11 >>>>>> 12.011 ; >>>>>> qtot 6.78 162 opls_557 9 EMI N5 95 0.15 >>>>>> 14.0067 ; >>>>>> qtot 6.93 163 opls_135 9 EMI C6 96 -0.17 >>>>>> 12.011 ; >>>>>> qtot 6.76 164 opls_136 9 EMI C7 97 -0.05 >>>>>> 12.011 ; >>>>>> qtot 6.71 165 opls_135 9 EMI C8 98 -0.17 >>>>>> 12.011 ; >>>>>> qtot 6.54 166 opls_564 9 EMI H9 99 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.75 167 opls_564 9 EMI H10 99 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 6.96 168 opls_563 9 EMI H11 99 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.17 169 opls_140 9 EMI H12 100 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.3 170 opls_140 9 EMI H13 100 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.43 171 opls_140 9 EMI H14 100 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.56 172 opls_140 9 EMI H15 101 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.69 173 opls_140 9 EMI H16 101 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.82 174 opls_140 9 EMI H17 102 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.88 175 opls_140 9 EMI H18 102 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.94 176 opls_140 9 EMI H19 102 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8 177 opls_561 10 EMI C 103 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 7.87 178 opls_561 10 EMI C2 104 -0.13 >>>>>> 12.011 ; >>>>>> qtot 7.74 179 opls_557 10 EMI N3 105 0.15 >>>>>> 14.0067 ; >>>>>> qtot 7.89 180 opls_558 10 EMI C4 106 -0.11 >>>>>> 12.011 ; >>>>>> qtot 7.78 181 opls_557 10 EMI N5 107 0.15 >>>>>> 14.0067 ; >>>>>> qtot 7.93 182 opls_135 10 EMI C6 108 -0.17 >>>>>> 12.011 ; >>>>>> qtot 7.76 183 opls_136 10 EMI C7 109 -0.05 >>>>>> 12.011 ; >>>>>> qtot 7.71 184 opls_135 10 EMI C8 110 -0.17 >>>>>> 12.011 ; >>>>>> qtot 7.54 185 opls_564 10 EMI H9 111 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.75 186 opls_564 10 EMI H10 111 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 7.96 187 opls_563 10 EMI H11 111 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.17 188 opls_140 10 EMI H12 112 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.3 189 opls_140 10 EMI H13 112 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.43 190 opls_140 10 EMI H14 112 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.56 191 opls_140 10 EMI H15 113 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.69 192 opls_140 10 EMI H16 113 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.82 193 opls_140 10 EMI H17 114 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.88 194 opls_140 10 EMI H18 114 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.94 195 opls_140 10 EMI H19 114 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9 196 opls_561 11 EMI C 115 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 8.87 197 opls_561 11 EMI C2 116 -0.13 >>>>>> 12.011 ; >>>>>> qtot 8.74 198 opls_557 11 EMI N3 117 0.15 >>>>>> 14.0067 ; >>>>>> qtot 8.89 199 opls_558 11 EMI C4 118 -0.11 >>>>>> 12.011 ; >>>>>> qtot 8.78 200 opls_557 11 EMI N5 119 0.15 >>>>>> 14.0067 ; >>>>>> qtot 8.93 201 opls_135 11 EMI C6 120 -0.17 >>>>>> 12.011 ; >>>>>> qtot 8.76 202 opls_136 11 EMI C7 121 -0.05 >>>>>> 12.011 ; >>>>>> qtot 8.71 203 opls_135 11 EMI C8 122 -0.17 >>>>>> 12.011 ; >>>>>> qtot 8.54 204 opls_564 11 EMI H9 123 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.75 205 opls_564 11 EMI H10 123 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 8.96 206 opls_563 11 EMI H11 123 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.17 207 opls_140 11 EMI H12 124 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.3 208 opls_140 11 EMI H13 124 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.43 209 opls_140 11 EMI H14 124 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.56 210 opls_140 11 EMI H15 125 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.69 211 opls_140 11 EMI H16 125 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.82 212 opls_140 11 EMI H17 126 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.88 213 opls_140 11 EMI H18 126 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.94 214 opls_140 11 EMI H19 126 0.06 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 10 215 opls_561 12 EMI C 127 -0.13 >>>>>> 12.011 >>>>>> ; >>>>>> qtot 9.87 216 opls_561 12 EMI C2 128 -0.13 >>>>>> 12.011 ; >>>>>> qtot 9.74 217 opls_557 12 EMI N3 129 0.15 >>>>>> 14.0067 ; >>>>>> qtot 9.89 218 opls_558 12 EMI C4 130 -0.11 >>>>>> 12.011 ; >>>>>> qtot 9.78 219 opls_557 12 EMI N5 131 0.15 >>>>>> 14.0067 ; >>>>>> qtot 9.93 220 opls_135 12 EMI C6 132 -0.17 >>>>>> 12.011 ; >>>>>> qtot 9.76 221 opls_136 12 EMI C7 133 -0.05 >>>>>> 12.011 ; >>>>>> qtot 9.71 222 opls_135 12 EMI C8 134 -0.17 >>>>>> 12.011 ; >>>>>> qtot 9.54 223 opls_564 12 EMI H9 135 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.75 224 opls_564 12 EMI H10 135 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 9.96 225 opls_563 12 EMI H11 135 0.21 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 10.17 226 opls_140 12 EMI H12 136 0.13 >>>>>> 1.008 ; >>>>>> qtot 10.3 227 opls_140 12 EMI H13 136 0.13 >>>>>> 1.008 >>>>>> ; >>>>>> qtot 10.43 228 opls_140 12 EMI H14 136 0.13 >>>>>> 1.008 ; >>>>>> qtot 10.56 229 opls_140 12 EMI H15 137 0.13 >>>>>> 1.008 ; >>>>>> qtot 10.69 230 opls_140 12 EMI H16 137 0.13 >>>>>> 1.008 ; >>>>>> qtot 10.82 231 opls_140 12 EMI H17 138 0.06 >>>>>> 1.008 ; >>>>>> qtot 10.88 232 opls_140 12 EMI H18 138 0.06 >>>>>> 1.008 ; >>>>>> qtot 10.94 233 opls_140 12 EMI H19 138 0.06 >>>>>> 1.008 ; >>>>>> qtot 11 >>>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> >>>>> >>>>> >>>>> Justin A. Lemkul >>>>> Ph.D. Candidate >>>>> ICTAS Doctoral Scholar >>>>> MILES-IGERT Trainee >>>>> Department of Biochemistry >>>>> Virginia Tech >>>>> Blacksburg, VA >>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>> >>>>> >>>>> >>>>> >>>>> ======================================== >>>>> -- >>>>> gmx-users mailing list [email protected] >>>>> 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 [email protected]. >>>>> Can't >>>>> post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> -- >>> ======================================== >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> >>> ======================================== >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. Can't >>> post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >>> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
