On 6/12/13 8:01 AM, Steven Neumann wrote:
60 types of atoms and 60 atoms in total belonging to one residue
The number of possible combinations is (N(N+1))/2, thus you get 1830 from 60
atom types.
-Justin
On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham <[email protected]>wrote:
How many atom *types* are there?
On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann <[email protected]
wrote:
and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann <[email protected]
wrote:
"All possible interactions = 60*60/2 = 1800. Where grompp takes another
30
from?
On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham <
[email protected]
wrote:
"Parameters for possible interactions" is not the same as
"interactions."
The latter depend on the configuration and cut-offs... grompp is not
doing
a neighbor search!
Mark
On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann <
[email protected]
wrote:
On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham <
[email protected]
wrote:
grompp is just enumerating the possible combinations of parameters
given
your inputs. Whether any of those will be used in the simulation
will
depend on whether atoms of given types are close enough and not
excluded.
Mark
I understand...but why for 60 mer polypeptide there are 1830
nonbonded
interactions ?
On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann <
[email protected]
wrote:
I got it. However,
I have 60 atoms in my chain all with given C6 and C12 with a
combination
rule 1. When running grompp:
Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are: 1 Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data
when changing nrexcl in my topology to 0:
Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are: 1 Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data
So if I exclude 1-3 interactions I have the same number of
nonbonded
parameters as well as 1-4 interactions. Can someone explain me
this
please?
On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <
[email protected]
wrote:
On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <
[email protected]>
wrote:
On 6/12/13 6:00 AM, Steven Neumann wrote:
Thank you. That means that e.g. when two LJ atoms of a
different
type
approaching each other the non bonded LJ potential energy
is a
sum
of
two
potentials of those atoms?
No, please refer to the Gromacs manual for discussion on
"combination
rules" and how they fit into the Lennard-Jones equation.
-Justin
I read it.
I used combination rule 1 in which C=4epsSig^6 and
A=4epsSig^12
-
So
that
means that when you provide in [atomtypes] in ffnonbonded
your C
and
A
values each atom has a specific LJ potential shape. Right?
So two of them approaching each other in my system will have
have
the
sum
of it.
Steven
On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <
[email protected]>
wrote:
On 6/12/13 5:30 AM, Steven Neumann wrote:
Dear Gmx Users,
Please, correct me if I am wrong. In ffnonbonded.itp
[ atomtypes ] - these are nonbonded parameters between
atoms
of
the
same
type
No, these are the nonbonded parameters that are used when
applying
combination rules between any atoms.
[ nonbond_params ] these are nonbonded parameters between
atoms
of
different type
No, these override combination rules.
[ pairtypes ] - 1-4 interactions
If that is correct why amber force filed has only
[atomtypes]
column?
How
nonbonded parameters are calculated between atoms of a
different
type?
The same with charmm - only [atomtypes ] and [pairtypes ]
are
provided.
Would you please explain?
Gromos force fields, for instance, have complex ways of
generating
nonbonded interactions that are not always the same for a
given
atomtype.
Other force fields just use straight combination rules
and
thus
never
need
[nonbond_params].
-Justin
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Research Scientist
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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