[gmx-users] hydrogen vibration leads to unphysical result

[tnle]

Hello fellow gromacs users,

I am running a system of hydroxylated silica (Si-O-H) pore with carbon
dioxide and propane. When I fix all the atoms of the solid, the gases can
move freely in and out the pore. However, if I allow the hydrogen to vibrate
(the way it's supposed to be), all the gases got stuck in the middle of the
pore. I've been trying to fix this problem for months. If anyone had similar
problem before with a solution, please help me out!

Here is the force fields: (silica - clayff ; propane and CO2 - trappe)

[ moleculetype ]
;  name  nrexcl
   SSOH       2
 
[ atoms ]
;   nr  type    resnr    residu   atom    cgnr     charge
     1    SI        1      SSOH     SI       1     2.1000
     2    ON        1      SSOH     ON       2    -0.9500
     3     H        1      SSOH      H       3     0.4250  

[ bonds ]
;   ai    aj    funct        c0          c1
     2     3        1       0.1      463700

[ angles ]
;   ai    aj    ak    funct         c0       c1
     1     2     3        1     109.47   251.04

[ exclusions ]
2 3


[ moleculetype ]
; Name nrexcl
PRO       3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     
     1       CH3     1  PRO       C1     1    0.000  
     2       CH2     1  PRO       C2     2    0.000  
     3       CH3     1  PRO       C3     3    0.000  
   
[ constraints ]
;  ai    aj funct        b0      
1 2 1 0.154  
2 3 1 0.154  
 
[ angles ]
; ai  aj  ak  fu    
1 2 3 1 114.000     519.6417
 

[ moleculetype ]
; molname nrexcl
CDO 2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge      
     1   CD   1 CDO     CD      1     0.7    
     2  OD1    1 CDO    OD1     2    -0.35    
     3  OD2   1 CDO    OD2    3    -0.35    

 
[ constraints ]
;  ai    aj funct        b0      
    1     2     1     0.116
    2     3     1     0.232
    1     3     1     0.116



Thank you very much!!!! 

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