On 2011-03-18 12.23, Cen-Feng Fu wrote:
Hi David,
Thanks for your suggestion. Now I have complete the topology files for
benzyl alcohol and phenylethanol.
However, I have a new doubt. In your topology file for benzyl alcohol,
; ring_180
    1     3     5     7     1   180     4.6     2
    3     5     7     9     1   180     4.6     2
    5     7     9    11     1   180     4.6     2
    7     9    11     1     1   180     4.6     2
    9    11     1     3     1   180     4.6     2
   11     1     3     5     1   180     4.6     2
is this section necessary? If I don't put this section in the file, is
the results still correct?

This is for you to find out based on the original article. There may or may not be a reference in the atomtypes.atp. Otherwise check generic OPLS articles.
Thanks!

     > Dear Users,
     > I am trying to do some simulations for liquid benzyl alcohol and
     > phenylethanol.  I want to use the OPLS-AA force field. However, I
    don't
     > know which parameters should be used for atoms in these two
    molecules.
     > In the ffnonbonded.itp file for OPLS-AA, which parameters (opls_xxx)
     > should I use. Could anyone give some suggestions? Thanks!
    Check both atomtypes.atp and the above file. Then you will be able to
    find out.

    I' attaching benzyl alcohol. Please double check before using it.
     >
     > --
     >
    ----------------------------------------------------------------------
     > Cen-Feng Fu
     > Department of Chemical Physics
     > University of Science and Technology of China
     > Hefei, Anhui, 230026, P.R.China
     >
    ----------------------------------------------------------------------
     >


    --
    David van der Spoel, Ph.D., Professor of Biology
    Dept. of Cell & Molec. Biol., Uppsala University.
    Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
    sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
    http://folding.bmc.uu.se
    -------------- next part --------------
    [ moleculetype ]
    ; Name            nrexcl
    benzyl-alcohol                 3

    [ atoms ]
    ;   nr       type  resnr residue  atom   cgnr     charge       mass
      typeB    chargeB      massB
             1  opls_145         1       LIG         C         1
      -0.115    12.011
             2  opls_146         1       LIG         H         2
    0.115     1.008
             3  opls_145         1       LIG         C         3
      -0.115    12.011
             4  opls_146         1       LIG         H         4
    0.115     1.008
             5  opls_145         1       LIG         C         5
      -0.115    12.011
             6  opls_146         1       LIG         H         6
    0.115     1.008
             7  opls_145         1       LIG         C         7
      -0.115    12.011
             8  opls_146         1       LIG         H         8
    0.115     1.008
             9  opls_145         1       LIG         C         9
      -0.115    12.011
            10  opls_146         1       LIG         H        10
    0.115     1.008
            11  opls_221         1       LIG         C        11
      -0.055    12.011
            12  opls_218         1       LIG         C        12
    0.2    12.011
            13  opls_140         1       LIG         H        13
    0.060     1.008
            14  opls_140         1       LIG         H        14
    0.060     1.008
            15  opls_154         1       LIG         O        15
      -0.683   15.9994
            16  opls_155         1       LIG         H        16
    0.418     1.008

    [ bonds ]
    ;  ai    aj funct            c0            c1            c2
        c3
        1     2     1
        1     3     1
        1    11     1
        3     4     1
        3     5     1
        5     6     1
        5     7     1
        7     8     1
        7     9     1
        9    10     1
        9    11     1
       11    12     1
       12    13     1
       12    14     1
       12    15     1
       15    16     1

    [ pairs ]
    ;  ai    aj funct            c0            c1            c2
        c3
        1     6     1
        1     7     1
        1    10     1
        1    13     1
        1    14     1
        1    15     1
        2     4     1
        2     5     1
        2     9     1
        2    12     1
        3     8     1
        3     9     1
        3    12     1
        4     6     1
        4     7     1
        4    11     1
        5    10     1
        5    11     1
        6     8     1
        6     9     1
        7    12     1
        8    10     1
        8    11     1
        9    13     1
        9    14     1
        9    15     1
       10    12     1
       11    16     1
       13    16     1
       14    16     1

    [ angles ]
    ;  ai    aj    ak funct            c0            c1            c2
              c3
        2     1     3     1
        2     1    11     1
        3     1    11     1
        1     3     4     1
        1     3     5     1
        4     3     5     1
        3     5     6     1
        3     5     7     1
        6     5     7     1
        5     7     8     1
        5     7     9     1
        8     7     9     1
        7     9    10     1
        7     9    11     1
       10     9    11     1
        1    11     9     1
        1    11    12     1
        9    11    12     1
       11    12    13     1
       11    12    14     1
       11    12    15     1
       13    12    14     1
       13    12    15     1
       14    12    15     1
       12    15    16     1

    [ dihedrals ]
    ;  ai    aj    ak    al funct            c0            c1
      c2            c3            c4            c5
        2     1     3     4     3
        2     1     3     5     3
       11     1     3     4     3
       11     1     3     5     3
        2     1    11     9     3
        2     1    11    12     3
        3     1    11     9     3
        3     1    11    12     3
        1     3     5     6     3
        1     3     5     7     3
        4     3     5     6     3
        4     3     5     7     3
        3     5     7     8     3
        3     5     7     9     3
        6     5     7     8     3
        6     5     7     9     3
        5     7     9    10     3
        5     7     9    11     3
        8     7     9    10     3
        8     7     9    11     3
        7     9    11     1     3
        7     9    11    12     3
       10     9    11     1     3
       10     9    11    12     3
        1    11    12    13     3
        1    11    12    14     3
        1    11    12    15     3
        9    11    12    13     3
        9    11    12    14     3
        9    11    12    15     3
       11    12    15    16     3
       13    12    15    16     3
       14    12    15    16     3

    ; added, improper
       1     11     3     2     1   180     4.6     2
       3      1     5     4     1   180     4.6     2
       5      3     7     6     1   180     4.6     2
       7      5     9     8     1   180     4.6     2
       9      7    11    10     1   180     4.6     2
      11      9     1    12     1   180     4.6     2
    ; ring_180
        1     3     5     7     1   180     4.6     2
        3     5     7     9     1   180     4.6     2
        5     7     9    11     1   180     4.6     2
        7     9    11     1     1   180     4.6     2
        9    11     1     3     1   180     4.6     2
       11     1     3     5     1   180     4.6     2


--
----------------------------------------------------------------------
Cen-Feng Fu
Department of Chemical Physics
University of Science and Technology of China
Hefei, Anhui, 230026, P.R.China
----------------------------------------------------------------------



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
--
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