[gmx-users] own forcefield and pairs

[Lubos Vrbka]

hi guys,

i have (probably stupid) question, but i'm struggling with it for some 
days now without success...

i want to create a forcefield. everything is ok except the pairs, of 
course. the forcefield should be used for simulations with a specific 
water model (nada and van der eerden 6 center) - works fine - and some 
'contaminant' - nacl (that's easy) and probably simple aliphatic 
alcohols - and here comes the problem.

relevant excerpts from the topology are pasted at the end (some numbers 
are probably wrong, so don't count on the factual correctness of the 
potential).

the alcohol 'strategy' is taken from the ffgmx file (i.e. CH3 as a 
single atom). now if i use gen-pairs yes, i guess i shouldn't have the 
[pairs] section for the 5OL. with gen-pairs=no, i should probably have 
the [pairs] section for all 1-4 interactions. but what values should be 
given for the [pairs] section c6 and c12 parameters? the example in 
manual (urea) has all zeroes there, however i don't know whether it's 
intentional or not.

funny enough, all 3 possibilities (gen-pairs yes, no [pairs]; gen-pairs 
no, [pairs]; gen-pairs no, no [pairs]) give me the same numbers... but 
that might be as well as a consequence of the initial structure...

so i'm confused now and i don't know what setup is the correct one. i 
would be really glad if someone could point me in the right direction....

thanks in advance. best regards,
lubos

 >>>>>>>>>>>>>>> excerpts from the topology follow

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
   1             2               yes             1.0     1.0

;
[ atomtypes ]
...
;
; organic contaminant
ffv_ch2 CH2     14.02700        0.000   A       0.90975E-02     0.35333E-04
ffv_ch3 CH3     15.03500        0.000   A       0.88765E-02     0.26150E-04
ffv_oh  OH      15.99940        0.000   A       0.22617E-02     0.15062E-05
ffv_hh  HH       1.00800        0.000   A       0.00000E+00     0.00000E+00

[ moleculetype ]
; molname       nrexcl
   5OL           3

[ atoms ]
; id    at type res nr  resname at name cg nr   charge
1       ffv_hh  1       5OL     HH      1        0.398
2       ffv_oh  1       5OL     OH      1       -0.548
3       ffv_ch2 1       5OL     C01     1        0.150
4       ffv_ch2 1       5OL     C02     1        0.000
5       ffv_ch2 1       5OL     C03     1        0.000
6       ffv_ch2 1       5OL     C04     1        0.000
7       ffv_ch3 1       5OL     C05     1        0.000

[ bonds ]
; ai    aj      funct   b0      kb
  1      2       1       0.10000 313800.
  2      3       1       0.14300 334720.
  3      4       1       0.15300 334720.
  4      5       1       0.15300 334720.
  5      6       1       0.15300 334720.
  6      7       1       0.15300 334720.

[ angles ]
; ai    aj      ak      funct th0       cth
  1      2       3       1       109.500 397.480
  2      3       4       1       109.500 460.240
  3      4       5       1       111.000 460.240
  4      5       6       1       111.000 460.240
  5      6       7       1       111.000 460.240
[ dihedrals ]
; ai    aj      ak      al      funct   phi     cp      mult
  1      2       3       4       1       0.000   1.255   3
  2      3       4       5       1       0.000   5.858   3
  3      4       5       6       1       0.000   5.858   3
  4      5       6       7       1       0.000   5.858   3

;[ pairs ]
; ai    aj      funct   c6      c12
; 1     4       1       0.0     0.0
; 1     5       1       0.0     0.0
; 1     6       1       0.0     0.0
; 1     7       1       0.0     0.0
; 2     5       1       0.0     0.0
; 2     6       1       0.0     0.0
; 2     7       1       0.0     0.0
; 3     6       1       0.0     0.0
; 3     7       1       0.0     0.0
; 4     7       1       0.0     0.0

-- 
Lubos _ at _"
http://www.lubos.vrbka.net