[gmx-users] free energy
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 11 01:40:03 CET 2010
On 1/10/10 7:02 PM, Nilesh Dhumal wrote:
> 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).
Under Gromacs 4.0.x, you should be able to leave the topology alone entirely.
No B state should need to be defined explicitly.
>
> I am using default parameters for "couple-lambda0" and "couple-lambda1".
The default behavior is vdw-q, is it not? Then what you're doing still doesn't
make sense to me entirely, because no decoupling would even be specified if that
is the case. Can you post your actual .mdp file (mdout.mdp might be better if
you're leaving it up to grompp to decide the defaults, etc)? I'll admit I
haven't done much with the 4.0 free energy code, but it seems to me that with an
unaltered topology (no B state explicitly defined) you should be able to set the
following in the .mdp file:
couple-lambda0 = vdw-q
couple-lambda1 = vdw
...to decouple only Coulombic interactions, and likewise:
couple-lambda0 = vdw
couple-lambda1 = none
...to decouple van der Waals.
Perhaps someone can correct me if I've gotten this wrong.
> For one of my simulation (glucose + ionic liquids) I am getting solvation
> free energy 35.5 Kcal/mol.
> Is it too high?
>
Not a clue. Isn't that what you're trying to figure out? Is there any sort of
literature value for such a parameter? In any case, it's more plausible than
your original value.
-Justin
> 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 gmx-users at 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-request at gromacs.org.
>>>>>> 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 gmx-users at 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-request at gromacs.org. 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 gmx-users at 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-request at gromacs.org. 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
========================================
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