Hello! Sorry to bother you again, but I have another question. I have written a topology file of two water molecules to test the pair interaction. Here is part of my topology file:
[ moleculetype ] SOL 2 [ atoms ] 1 opls_116 1 SOL OW 1 -0.82 2 opls_117 1 SOL HW1 1 0.41 3 opls_117 1 SOL HW2 1 0.41 4 opls_116 2 SOL OW 2 -0.82 5 opls_117 2 SOL HW1 2 0.41 6 opls_117 2 SOL HW2 2 0.41 [ settles ] 1 1 0.1 0.16330 4 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 4 5 6 5 4 6 6 4 5 [ exclusions ] 1 4 [ pairs ] 1 4 1 I have also changed the fudgeLJ and fudgeQQ to 1.0. Originally, there is no pair interaction in this system. First I did a simulation when the last 4 lines were removed, that is, I treated all the interactions as non-bonded interactions. Then I added the last 4 lines to specify the normal non-bonded interaction between atom 1 and 4 as pair interaction in order to see whether that will affect the result. It turns out that the results for the two cases are different. So did I miss something, or are pair interactions and non-bonded interactions treated differently by GROMACS? Thanks in advance. 2009/7/28 Mark Abraham <mark.abra...@anu.edu.au> > Lee Soin wrote: > >> So there is no place to specify electrostatic interactions for pair >> interactions? >> > > No. The charges are specified in the [ atoms ] directive. Read the example > in chapter 5. > > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- SUN Li Department of Physics Nanjing University, China
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