[gmx-users] OPLSAA parameters
Justin A. Lemkul
jalemkul at vt.edu
Fri Nov 21 05:03:25 CET 2008
> Thank you Justin.
> Can you tell me how i can find the link between atom names and atom types?
That is listed in the .rtp:
; name type charge cgnr
CG opls_235 0.500 3
> The thing I wanna do is to figure out the bond parameters(b0,bk), and so
> the angle, dihedral parameters in oplsaa FF.
> Is it possible to give me some examples, such as the bond between CG and
> OG1 in [ASN] in ffoplsaa.rtp?
The easiest thing I can think of to do is use the -pp flag with grompp, and look
at the processed topology, which will explicitly print the parameters.
Otherwise, you have to interpret atom types from the .atp and apply them to
generic atom types in ffoplsaabon.itp (which can take quite a bit of time!), so
let grompp do the work for you, and use that as a reference.
> Justin A. Lemkul wrote:
>> friendli wrote:
>>> Dear all,
>>> To understand the exact parameters used in oplsaa force field, I read
>>> the ffoplsaa*.*** files.
>>> But I can not find all the corresponding atom types in the
>>> ffoplsaa.rtp and ffoplsaabon.itp files.
>>> for example, in rtp file, there is a bond between atom type CG and
>>> OG1. But in *bon.itp, there is no such atom types CG or OG1 in the
>>> [bondtypes]. where is the bond constants etc kept? and how Gromacs
>>> find them?
>> CG and OG1 are atom names, not atom types. The force field can
>> determine bonds based on atom types. As long as they are recognized
>> atom types and parameters for such a bond are present, there will be
>> no problem.
>>> Can anybody give a hint for this?
>>> thanks in advance
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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