[gmx-users] Virtual sites LJ/mass

[dakoenig]

Dear Gromacs-Experts,

for my simulations of pure hexane (united atom model) I would like to
separate the mass and the interaction parameters of the CH3. So far I tried
several different setups by using virtual sites but none of them is working.
I hope somebody can help.

Here is some background information:

My "normal" hexane molecule looks like that:
CH3-CH2-CH2-CH2-CH2-CH3

The molecule with the separated mass and interaction parameters (LJ) should
look like that:
LJ[CH3]-Mass[CH3]-CH2-CH2-CH2-CH2-Mass[CH3]-LJ[CH3]

Is a setup like that possible?

Here is my topology file:

[ atomtypes ]
;name	 at.num	   mass     charge   ptype	 V	          W
CH3            6            15.0350      0        A             0              
0
VSI             6            0               0        V           
CH2            6            14.0270      0        A             

[ moleculetype ]
; Name    nrexcl
Hexane      4

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       VSI     1  HEX     VSI     1    0.0    0
     2       CH3     1  HEX     CH3     1    0.0    15.0350   
     3       CH2     1  HEX     CH2     2    0.0    14.0270   
     4       CH2     1  HEX     CH2     2    0.0    14.0270   
     5       CH2     1  HEX     CH2     3    0.0    14.0270   
     6       CH2     1  HEX     CH2     3    0.0    14.0270   
     7       CH3     1  HEX     CH3     4    0.0    15.0350
     8       VSI     1  HEX     VSI     4    0.0    0 

[ bonds ]
; ai  aj  fu    b_0	k_b
   2   1   2    0.0066  715000000
   3   2   2    0.153   715000000
   4   3   2    0.153   715000000
   5   4   2    0.153   715000000
   6   5   2    0.153   715000000
   7   6   2    0.153   715000000
   8   7   2    0.0066  715000000

[ virtual_sites3 ]
; Site  from          fu    theta    d
  1     4  3  2       3     180      0.0066
  8     5  6  7       3     180      0.0066

[ pairs ]
;ai  aj  fu
  1   6   1
  3   8   1

[ constraints ]
;  ai  aj  fu   b
   2   3   1    0.153
   3   4   1    0.153
   4   5   1    0.153
   5   6   1    0.153
   6   7   1    0.153
   
[ angles ]
; ai  aj  ak  fu    theta     k_theta
   1   2   3   2    180       52000
   2   3   4   2    
   3   4   5   2    
   4   5   6   2   
   5   6   7   2    
   6   7   8   2    180       52000

[ dihedrals ]
; ai  aj  ak  al  fu      C_1     C_2       C_3       C_4
   5   4   3   1   5      
   6   5   4   3   5      
   8   6   5   4   5

By executing an energy minimization the hexane molecules are folding
themselves together. Since all simulations with "normal" hexane molecules
are working fine, I guess there is no problem with the .gro or .mdp file.

Any help is highly appreciated. Thank you very much!

Merry X-Mas and happy new year :)

Daniel  




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