[gmx-users] 100-quartz force field for GROMACS using CGenFF

Ivan Gladich igladich at sissa.it
Sun Mar 5 12:56:26 CET 2017


Dear all,

I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated 
interface using GROAMCS.

Force field parameters and structure are available in CHARMM 
(http://mackerell.umaryland.edu/charmm_ff.shtml) and  reported in the 
supplemental material of Lopes, P.E.M., Murashov, V., Tazi, M., Demchuk, 
E. and MacKerell, Jr., A.D. "Development of an Empirical Force Field for 
Silica. Application to the Quartz-Water Interface," Journal of Physcial 
Chemistry B 110: 2782-2792, 2006.

Since I am not familiar with CHARMM force field (and crystal simulations 
as well), my plan was to create the FF in CHARMM and then convert it to 
GMX format.  I copied the quartz (100) structure reported in the paper 
above, converting it in .mol2 format, adding PBC information (see mol2 
attached below).

Then I tried using CHARMM General Force Field (CGenFF) program  
(https://cgenff.paramchem.org) uploading my .mol2 file. If I understand 
correctly, the quartz parameters reported in the paper above should be 
present in CGenFF program. However, I am getting error of the type:
"Now processing molecule Q100 ... attype warning: element not 
supported;skipped molecule."

Since I read from this mailing list that some of you currently use 
CGenFF, I would like to ask whether some of you have some advise on
how to get this force field for this structure running in GROAMCS, using 
CGenFF or any other alternative way.

Thank you very much for any possible help or hint.

Ivan



@<TRIPOS>MOLECULE
Q100
43   40    3
SMALL
USER_CHARGES


@<TRIPOS>ATOM
       1 Si          0.1700    1.0500   13.0600 Si        1  Si         
0.0000
       2 Si1         0.1700    3.5000   17.3100 Si        1  Si         
0.0000
       3 Si2         0.1700    1.0500   21.5600 Si        1  Si         
0.0000
       4 Si3         0.1700    3.5000   25.8100 Si        1  Si         
0.0000
       5 O           0.8000    1.5400   11.6500 O         2   O         
0.0000
       6 O1          0.8000    3.9900   15.9000 O         2   O         
0.0000
       7 O2          0.8000    1.5400   20.1500 O         2   O         
0.0000
       8 O3          0.8000    3.9900   24.4100 O         2   O         
0.0000
       9 O4          4.4000    2.0500   13.5000 O         2   O         
0.0000
      10 O5          4.4000    4.5000   17.7500 O         2   O         
0.0000
      11 O6          4.4000    2.0500   22.0100 O         2   O         
0.0000
      12 O7          4.4000    4.5000   26.2600 O         2   O         
0.0000
      13 O8          4.9400    4.5000   12.7700 O         2   O         
0.0000
      14 O9          4.9400    2.0500   17.0300 O         2   O         
0.0000
      15 O10         4.9400    4.5000   21.2800 O         2   O         
0.0000
      16 O11         4.9400    2.0500   25.5300 O         2   O         
0.0000
      17 O12         1.3400    0.9400   14.1400 O         2   O         
0.0000
      18 O13         1.3400    3.3900   18.3900 O         2   O         
0.0000
      19 O14         1.3400    0.9400   22.6400 O         2   O         
0.0000
      20 O15         1.3400    3.3900   26.9000 O         2   O         
0.0000
      21 Si4         1.9700    2.4200   11.0100 Si        1  Si         
0.0000
      22 Si5         1.9700   -0.0400   15.2600 Si        1  Si         
0.0000
      23 Si6         1.9700    2.4200   19.5200 Si        1  Si         
0.0000
      24 Si7         1.9700   -0.0400   23.7700 Si        1  Si         
0.0000
      25 Si8         1.9700    2.4200   28.0200 Si        1  Si         
0.0000
      26 Si9         3.7700    3.5000   13.2200 Si        1  Si         
0.0000
      27 Si10        3.7700    1.0500   17.4700 Si        1  Si         
0.0000
      28 Si11        3.7700    3.5000   21.7200 Si        1  Si         
0.0000
      29 Si12        3.7700    1.0500   25.9800 Si        1  Si         
0.0000
      30 O16         2.6000    3.3900   12.1400 O         2   O         
0.0000
      31 O17         2.6000    0.9400   16.3900 O         2   O         
0.0000
      32 O18         2.6000    3.3900   20.6400 O         2   O         
0.0000
      33 O19         2.6000    0.9400   24.8900 O         2   O         
0.0000
      34 O20         3.1400    3.9900   14.6200 O         2   O         
0.0000
      35 O21         3.1400    1.5400   18.8800 O         2   O         
0.0000
      36 O22         3.1400    3.9900   23.1300 O         2   O         
0.0000
      37 O23         3.1400    1.5400   27.3800 O         2   O         
0.0000
      38 H           1.3400    3.3900    9.8900 H         3   H         
0.0000
      39 H1          3.1400    1.5400   10.3700 H         3   H         
0.0000
      40 O24         0.8000    1.5400   28.6600 O         2   O         
0.0000
      41 O25         2.6000    3.3900   29.1400 O         2   O         
0.0000
      42 H2          0.8000    1.5400   29.7600 H         3   H         
0.0000
      43 H3          2.6000    3.3900   30.2400 H         3   H         
0.0000
@<TRIPOS>BOND
      1    1    5 1
      2    1   17 1
      3    2    6 1
      4    2   18 1
      5    3    7 1
      6    3   19 1
      7    4    8 1
      8    4   20 1
      9    5   21 1
     10    7   23 1
     11    9   26 1
     12   11   28 1
     13   13   26 1
     14   14   27 1
     15   15   28 1
     16   16   29 1
     17   17   22 1
     18   18   23 1
     19   19   24 1
     20   20   25 1
     21   21   30 1
     22   21   38 1
     23   21   39 1
     24   22   31 1
     25   23   32 1
     26   23   35 1
     27   24   33 1
     28   25   37 1
     29   25   40 1
     30   25   41 1
     31   26   30 1
     32   26   34 1
     33   27   31 1
     34   27   35 1
     35   28   32 1
     36   28   36 1
     37   29   33 1
     38   29   37 1
     39   40   42 1
     40   41   43 1
@<TRIPOS>SUBSTRUCTURE
      1  Si         1 GROUP             0       ****    0 ROOT
      2   O         5 GROUP             0       ****    0 ROOT
      3   H        38 GROUP             0       ****    0 ROOT
@<TRIPOS>FF_PBC
v1.0 1  0.0 0.0 0.0 4.914    4.914   40.000 none



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