[gmx-users] Subject: Interfacial System - Topology file

[Robson P. S. Peguin]

Hi everybody,

I'm trying GROMACS by the 1st time with an interfacial system: HFA and Water. I had created the topology file manually and  the HFA section had worked fine for an energy minimization of pure HFA and air. However, the geometry of HFA molecules become distorted during interfacial energy minimization, but the box doesn't collapse. I can see from VMD visualization package that the geometry is distorted. I would like to know if there is anything wrong with my topol.top file (described bellow). I had added the opls atoms and LJ parameters in the ffoplsanb.itp and; bonds, angles and dihedral in  ffoplsaabon.tip. Since initially I'm trying to simplify the system,  my HFA molecules will have a rigid geometry. So, angles and dihedral specifications became comments in the ffoplsaabon.tip file. Pls, let me know if I'm in the right track. Thanks
#include "ffoplsaa.itp"

[ moleculetype ]
; molname    nrexcl
SOL        2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge 
     1    opls_970   1    SOL    HW1      1     0.4238 
     2    opls_971   1    SOL    HW2      1     0.4238 
     3    opls_972   1    SOL    OW       1    -0.8476 

[ bonds ]
; i    j    funct   
3    1    1   
3    2    1   

[ angles ]
; i    j    k   
1    3    2   

[ moleculetype ]
; name  nrexcl
HFA        3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge
     1  opls_966   1    HFA    FF       1    -0.30
     2  opls_967   1    HFA    CH       1     0.24
     3  opls_969   1    HFA    HF       1     0.03
     4  opls_969   1    HFA    HF       1     0.03
     5  opls_968   1    HFA    CF       1     0.90
     6  opls_966   1    HFA    FF       1    -0.30
     7  opls_966   1    HFA    FF       1    -0.30
     8  opls_966   1    HFA    FF       1    -0.30

[ constraints ]
;  ai    aj funct   b0
    1     2     1     0.13600 
    3     2     1     0.10900
    4     2     1     0.10900
    2     5     1     0.15290
    5     6     1     0.13600
    5     7     1     0.13600
    5     8     1     0.13600
    1     4     1     0.20228
    3     4     1     0.17695
    8     1     1     0.28042
    8     6     1     0.22022
    6     7     1     0.22028
    6     4     1     0.32963

[ system ]
HFA and water

[ molecules ]
SOL        735
HFA          156
 

-- 
Robson Peguin, PhD Student
Wayne State University, ChE
Detroit - MI, 48201 - USA
2015 MEB, (313) 577-1416
2348 ENG, (313) 577-5765
Fax: (313) 577-3810
e-mail: robson_peguin at wayne.edu
http://chem1.eng.wayne.edu/~sdr/
_________________________________________________
Robson P. S. Peguin, PhD Student
Wayne State University
Department of Chemical Engineering and Materials Science
Detroit - MI, 48201 - USA
2015 MBE, phone: (313) 577-1416
2348 ENG, phone: (313) 577-5765
Fax: (313)577-3810
e-mail: robson_peguin at wayne.edu
http://chem1.eng.wayne.edu/~sdr/