[gmx-users] Subject: Interfacial System - Topology file
Robson P. S. Peguin
ao8215 at wayne.edu
Thu Apr 20 19:13:40 CEST 2006
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/
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