Thanks Justin.The simulation is indeed with CHARMM and the error went away
when I used sigma and epsilon instead of C6 and C12. This run was for no
scaling but now I can design the rest of the simulation without scaling the
C12 term.
Thanks again
Pooja
On Mon, Nov 1, 2010 at 9:02 PM, Justin A. Le
Sai Pooja wrote:
Hi,
Restating that I was trying to scale the Protein Solvent interactions, I
added a new section to the ffnonbonded.itp file. This is what the
section looks like
[ nonbond_params ]
C OWT31 0.00335276 0.0518
CA OWT31 0.00266209
Hi,
Restating that I was trying to scale the Protein Solvent interactions, I
added a new section to the ffnonbonded.itp file. This is what the section
looks like
[ nonbond_params ]
C OWT31 0.00335276 0.0518
CA OWT31 0.00266209 0.0411
CC OWT3
Hi All,
I want to exclude attractive Lennard-Jones interactions between atoms that i
defined in the ffamber99nb.itp file.
the properties of the dummy atom which I defined are:
*amber99_69X 0. 0. A 3.39967e-01 3.59824e-02* ;
(i.e., Sigma=3.39967e-01 and Epsilon=3.59824e-02
The [ nonbond_params ] section is located in the nb.itp file of your chosen
force field. The error comes from the fact that you have likely tried to
introduce an additional [ nonbond_params ] directive within your .top file,
which is incorrect. You cannot have multiple entries for these dire
Thank you Justin,
I didn't understand though where can I edit the [ nonbond params ] section?
Is there a better way to define pairs with no LJ attraction that will ignore
the settings in the *nb.itp file?
Cheers,
Amir
On Mon, Jul 26, 2010 at 5:31 PM, Justin A. Lemkul wrote:
>
>
> Amir Marcovit
Amir Marcovitz wrote:
Hi,
my system is composed of two molecules, each is composed of a 36 carbon
like dummy atoms i defined in the amber files (i.e., has the LJ
parameters of a carbon)
I'm interested in eliminating the attractive Lennard-Jones interactions
between the dummy atoms , such th
Hi,
my system is composed of two molecules, each is composed of a 36 carbon like
dummy atoms i defined in the amber files (i.e., has the LJ parameters of a
carbon)
I'm interested in eliminating the attractive Lennard-Jones interactions
between the dummy atoms , such that only the repulsive terms w
On Sat, 8 Jul 2006, ARGYRIOS KARATRANTOS wrote:
>HI Gromacs users,
>
>my question is if i have to denote under the [nonbond_params] same non bonded
>atoms in a polymeric chain, such as C-C nonbonded interactions.
>
>i am giving the lennard jones parameters in the [atomtypes] for carbon(C).
>
>do
HI Gromacs users,
my question is if i have to denote under the [nonbond_params] same non bonded
atoms in a polymeric chain, such as C-C nonbonded interactions.
i am giving the lennard jones parameters in the [atomtypes] for carbon(C).
do i have to write again the nonbonded interaction of C-C u
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