FW: [gmx-users] own forcefield and pairs

[Pakpoom Utta]

> Date: Thu, 31 Aug 2006 17:38:37 +0200> From: lists at vrbka.net> To: gmx-users at 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 _ at _"> http://www.lubos.vrbka.net> _______________________________________________> gmx-users mailing list    gmx-users at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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