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

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 23 18:30:25 CEST 2009

Vitaly V. Chaban wrote:
> Justin,
> I think force field specific syntax is important for the utilities
> like pdb2gmx or x2top but not for grompp which works with topol.top.
> Here, I do not use any "standard" force field but define everything
> myself from the very beginning. I believe this format (in topol.top)
> should be FF-independent.
> Am I not right?

You just have to be internally self-consistent.  You have to have some sort of 
[defaults] defined for whatever model you're making, so if your improper has 
type 2, then what you posted before should be fine.  If it is type 1 (like 
OPLS-AA), then impropers are defined like proper dihedrals, so the order will 
make a difference.


> Vitaly
>> 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).
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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