[gmx-users] forcefield validation

[Qin Shanshan]

Thanks very much for your patient explaination.It really is a question confusing me much. What I am interested in is inserting some organic molecules into lipid bilayers. Tieleman's lipid parameters have given out the interactive LJ parameters with ffgmx forcefield. So if I want to simulate lipid with tileman's force field I should use ffgmx for organic molecules. However I have to prove the ffgmx forcefield for organic molecules is correct too. Somebody prove this by calculating the new molecules' melting point or their structures in  solutions to compare with X-ray results. I found 
Monika Holtje's BBA article(Biochimica et Biophysica Acta 1511 (2001) 156^167), they simulated cholesterol and stearic acid and palmitic acid, constructing topology files using Gromos 87 forcefield , and put the Cholesterol topology on Gromacs website.They said " The geometries, conformations and configurations as they occur instandard GROMACS dynamics in vacuo and in water using the parameter set in this file, compared well with crystal structures". In their topology , they set the partial charge like this:


;   nr    type   resnr  residu    atom    cgnr    charge   ; total charge
     1     CH3       1    CHOL     C1        1     0
     2      CB       1    CHOL     C2        2     0
     3     CH2       1    CHOL     C3        3     0
     4     CH2       1    CHOL     C4        4     0
     5     CH1       1    CHOL     C5        5     0.14 ; charges adopted
     6      OA       1    CHOL     O6        5    -0.54 ; from Retinol in
     7      HO       1    CHOL     H         5     0.40 ; ffgmx.rtp
     8     CH2       1    CHOL     C8        6     0
     9      CB       1    CHOL     C9        7     0
    10    CR61       1    CHOL     C10       8     0
    11     CH2       1    CHOL     C11       9     0
    12     CH1       1    CHOL     C12      10     0
    13     CH1       1    CHOL     C13      11     0
    14     CH2       1    CHOL     C14      12     0
    15     CH2       1    CHOL     C15      13     0
    16      CB       1    CHOL     C16      14     0
    17     CH3       1    CHOL     C17      15     0
    18     CH1       1    CHOL     C18      16     0
    19     CH2       1    CHOL     C19      17     0
    20     CH2       1    CHOL     C20      18     0
    21     CH1       1    CHOL     C21      19     0
    22     CH1       1    CHOL     C22      20     0
    23     CH3       1    CHOL     C23      21     0
    24     CH2       1    CHOL     C24      22     0
    25     CH2       1    CHOL     C25      23     0
    26     CH2       1    CHOL     C26      24     0
    27     CH1       1    CHOL     C27      25     0
    28     CH3       1    CHOL     C28      26     0
    29     CH3       1    CHOL     C29      27     0

However when I use B3lyp/6-31G(d,p) to calculate mulliken distribution of cholesterol the charge distribution is rather different. How did they decide their partial charge? Is it customed to let alkane groups zero charged? Many articles didn't give out the validation procedure of their topologies in detail, are there some classic articles explaining how the forcefield we used today, such as OPLS, GROMOS, AMBER and CHARMM , developed? I want to know how they were deduced from the very beginning.

Any suggestion will be appreciated , thanks very much in advance.


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