[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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