[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
Mark.Abraham at anu.edu.au
Mon Aug 10 14:11:57 CEST 2009
Berk Hess wrote:
>> Date: Mon, 10 Aug 2009 20:52:31 +1000
>> From: Mark.Abraham at anu.edu.au
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
>> Lee Soin wrote:
>>> 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.
> That is incorrect.
> The exclusion line makes Gromacs excluded non-bonded interactions
> between atoms 1 and 4. The [ exclusions ] section, although itself
> "bonded" in some ways, has no relation at all with any other bonded
True, 5.4 does point out that there are (in a sense) two kinds of
exclusions, viz "The exclusions for bonded particles are generated by
grompp for neighboring atoms up to a certain number of bonds away, as
defined in the [ moleculetype ] section in the topology file (see
5.7.1).". Then the second paragraph goes on to point out the purpose of
[ exclusions ]: "Extra exclusions within a molecule can be added
manually in a [ exclusions ] section."
Perhaps the wording of this description could be improved, since the
sense of "[ exclusions ]" is actually "[ extra_exclusions ]"? A sentence
clarifying this before the full explanation would make things clearer:
Additional pairs of particles from which non-bonded interactions are to
be excluded may be indicated under this directive. Some exclusions for
bonded particles may be generated by grompp for neighbouring atoms...
Such extra exclusions within a molecule can be added manually in the [
exclusions ] list. Each line..."
>>> 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.
>> However, I believe you've merely added a second identical non-bonded
>> interaction between 1 and 4, so you will get different results regardless.
>> gmx-users mailing list gmx-users at gromacs.org
>> 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> Express yourself instantly with MSN Messenger! Download today it's FREE!
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users