2009/8/10 Mark Abraham <[email protected]> > Lee Soin wrote: > >> 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. >> > > Since there is no bonded interaction between 1 and 4, your second [ > exclusions ] directive will not have any effect. Read section 5.4. > Exclusions are cancellations only of interactions between bonded atoms. > > 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? >> > > mdrun is only reproducible if you tell it that you want it to be with > "mdrun -reprod". So it is possible that your observation of different > results is not (yet) meaningful.
Actually, I added the option "-reprod" and the results are reproducible. The results for the above-mentioned two cases are always different. So I am very confused. > > > However, I believe you've merely added a second identical non-bonded > interaction between 1 and 4, so you will get different results regardless. Then I tried to remove the two lines: [ exclusions ] 1 4 And retained the pair interaction that I have defined. But this lead to no difference in the simulation result. Is it that the "exclusion" of non-bonded interaction between atom 1 and atom 4 didn't work? On the other hand, in another set of simulations, I removed the pair interaction part: [ pairs ] 1 4 1 In this case, the presence and absence of the "exclusion" part do make a dramatic difference. So can this conclusion be drawn: the presence of a pair interaction automatically eliminates the corresponding non-bonded interaction? Mark _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- SUN Li Department of Physics Nanjing University, China
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