On 2011-04-21 03:54:09AM -0500, Jianguo Li wrote:
> Dear all,
>
> My molecule contains -CH=CH- fragment and I am trying to create the topology
> using Charmm FF. It seems that there is no improper dihedrals for -CH=CH-
> fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional
On 4/21/2011 6:54 PM, Jianguo Li wrote:
Dear all,
My molecule contains -CH=CH- fragment and I am trying to create the
topology using Charmm FF. It seems that there is no improper dihedrals
for -CH=CH- fragment in Charmm FF, while other FF (e.g., Amber or
OPLS) has additional improper dihedral
Dear all,
My molecule contains -CH=CH- fragment and I am trying to create the topology
using Charmm FF. It seems that there is no improper dihedrals for -CH=CH-
fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional
improper dihedrals terms for that fragment.
Could anybody
Pablo Englebienne wrote:
Hi all,
I have a question about the setting of improper dihedrals. I have a
pyrimidinone I want to use with the G53a5 force field, but I can't get
the ring to stay flat.
First question is: do all atoms in the planar ring need to have 3
subsituents? I.e., should an
Hi all,
I have a question about the setting of improper dihedrals. I have a
pyrimidinone I want to use with the G53a5 force field, but I can't get
the ring to stay flat.
First question is: do all atoms in the planar ring need to have 3
subsituents? I.e., should an explicit atom of type HC be
Vitaly V. Chaban 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
"
This section exists in a .tdb file, and analogous entries are in the .rtp for
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 t
Hi,
If you turn all bonds to constraints, and your system is infinitely
periodic, you probably don't even need impropers. The bond lengths can
only be satisfied in the plane. Adding impropers, straining your
molecule further into the configuration you think is proper, adds
forces that inevitable c
Darrell Koskinen wrote:
Dear GROMACS Gurus,
I assigned improper dihedrals to my graphene structuure but still see it
vibrating. Is this to be expected? I thought the purpose of improper
dihedrals was to keep planar structures planar.
There is still a force constant associated with the imp
Dear GROMACS Gurus,
I assigned improper dihedrals to my graphene structuure but still see it
vibrating. Is this to be expected? I thought the purpose of improper
dihedrals was to keep planar structures planar.
Here is a copy of a couple of sections of my topology file after
assigning the impr
Dear gmx-users,
I am confused about the exact formula for improper OPLS dihedrals in gromacs.
Is it periodic, e.g. V[1-cos(2x)], or harmonic, e.g. [V*(x-x0)^2]?
In ffoplsaa.rtp, it says in the Col 4 in the following the type of improper
dihedrals to be 1,
which I believe is a harmonic function. T
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