> Date: Thu, 31 Aug 2006 17:38:37 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] own forcefield and pairs
>
> 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 [EMAIL PROTECTED]"
> http://www.lubos.vrbka.net
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