[gmx-users] Re: Improper dihedrals, which way is correct?

[Justin A. Lemkul]

Vitaly V. Chaban wrote:
> Justin,
> 
> Thanks. These tidbits are too difficult for my brain to understand.
> Let's make the things easier. One has the below compound.
> 
> 7 -  1 - 2
>      /      \
>     6        3
>       \       /
>        5  - 4
> 
> I want the atom 7 to be located in the same plane with atoms 1 2 and
> 6. Then in topol.top:
> [ dihedrals ]
> atoms   func angle   constant
> 1 2 6 7   2    180      4.602
> 
> 

If this is the appropriate syntax for whatever force field you are using, yes. 
The reference atom is 1, and is held in a plane defined by 7, 2, and 6.  If atom 
7 is part of a planar group, you need to define a separate improper for it.

I mention the syntax because the order of atoms is different between, e.g., 
Gromos and OPLS (as are the implementations of the forms of the dihedrals).

> Will this line do what I want here?
> 

Try it and see :)

-Justin

> Vitaly
> 
> On Wed, Sep 23, 2009 at 1:53 PM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:
>> Hi,
>>
>> I have got confused with setting up improper dihedrals in the gromacs
>> topologies. In the manual (ver. 4.0) I see the section named [
>> impropers ] (page 104)
>> "
>> [ impropers ]
>> C O1 O2 CA
>> "
>>
>> but in the example system of the peptide
>> (share/gromacs/tutor/speptide) one finds defining impropers using the
>> second (in the same file) [ dihedrals ] section.
>> [ dihedrals ]
>> ;  ai    aj    ak    al funct            c0            c1
>> c2            c3
>>    1    23     5     6     1    improper_X_X_C_X
>>    1    23     5     7     1    improper_N_A_C1_C
>>    2     5     1     3     1    improper_X_X_M3_X
>>    2     5     1     4     1    improper_X_X_M3_X
>>
>> What is the correct way to work with improper dihedrals? I have four
>> sites, then angle value and then one force constant. What should my
>> topology line look like to accomplish that?
>>
>> I would also be very grateful if somebody could share some topology
>> with improper angles to understand how it works.
>>
>> Vitaly
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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