On 21/02/2012 4:36 AM, Lara Bunte wrote:
Hello
I use a charmm force field in gromacs. I almost finished my parametrization
except for Lennard-Jones parameters. For this parameters I want to adopt the
values in the charmm force field for the basic atom types.
In gromacs I have to put this parameters in the ffnonbonded.itp file in the
section [ pairtypes ] and I have to give following informations:
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
in example
CP1 CP1 1 0.338541512893 0.04184
Now here is a section of information given in the charmm documentation.
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
HN1 0.0 -0.0460 0.2245
HN2 0.0 -0.0460 0.2245
Sometimes CHARMM has special values for 1-4 interactions of some atom
types (in the last two columns) and sometimes not. CHARMM computes the
actual interaction parameters in the program. GROMACS has pre-computed
these in the [ pairtypes ] according to the combination rule. IIRC
there's some redundant entries where neither atom type has special 1-4
interactions. See manual 4.1.1 and 5.3.2 for how GROMACS needs these
computations to work.
The question is:
How to adopt the values in the charmm force field for the basic atom types in
gromacs? I do not really know what I have to write in the [ pairtypes ] section
in gromacs.
What's wrong with the existing contents of
$GMXLIB/share/top/charmm27.ff/ffnonbonded.itp?
Mark
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