[gmx-users] Explicit Topology Question

[Thomas Allen]

Let me include an example. I have three CG sites, labeled S, R, and C,  
and so a portion of a chain containing three of the monomers would  
appear schematically as:

S1   S2   S3
  |    |    |
R1---R2---R3  -> chain continues
  |    |    |
C1   C2   C3

The issue in this case is that both the angles R1-R2-C2 and C2-R2-R3  
are defined. The parameter set I have inherited (and don't have a good  
way to change) seems to only refer to the latter type of angle when  
considering C-R-R angle interactions (i.e. the angle is specified with  
reference to the 'forward' direction along the chain, so I only want  
C1-R1-R2 and C2-R2-R3 here, along with the obvious continuation with  
C3 and later monomer units).

What I would like is some way to prevent GROMACS from generating the  
'backward' angle R1-R2-C2, which it currently does automatically. I  
considered your suggestion regarding the bonds, but the only ones I  
have defined and which show up in the topol.top file after processing  
are those required to hold the structure together as shown above; I  
can't find any redundant bonds in this case.

I realize what I'm asking for is probably somewhat contrary to  
standard usage in all-atom MD, but I was wondering if there was a way  
to support it anyhow.

Thanks,
Tom

Quoting Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Do you mean on the same three atoms, or that each of your beads has such
> "backward" angles? I haven't looked at that code in a long time, but it's
> probably pretty dumb - two bonds with a common atom generate an angle, so
> if you don't want the angle, don't specify redundant bonds?
>
> Mark
>
> On Mon, Jan 9, 2017 at 7:30 PM Thomas Allen <thomas.c.allen at rice.edu> wrote:
>
>> Hello all,
>>
>> I'm currently implementing a simple polymer coarse-grained model in
>> GROMACS through some modifications to the OPLS force field. An issue
>> I'm having is that there are certain angles generated when parsing the
>> topology file which I don't want. For example, assuming atoms A, B, C,
>> I get the angles:
>>
>> A B +C
>>
>> and
>>
>> -C B A
>>
>> However, I only want the forward version (A B +C). I know that
>> unwanted dihedrals can be excluded by topology file settings, and I
>> know that CHARMM has settings which allow only certain angles or other
>> interactions specified explicitly in the topology file entry to be
>> generated for a given residue. I was wondering if there was an
>> equivalent when using GROMACS, or if I will have to come up with some
>> clever text editing to fix the issue in the topol.top file itself.
>>
>> Thanks,
>> Tom Allen
>>
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