Be careful if you are going to change the parameter to zero , because there
is a combination rule that defines the usage of C6 and C12. and this
combination rule is defined in the *.itp file
On Mon, Sep 27, 2010 at 8:34 PM, wrote:
> How can I do that using OPLSAA, because in the nb.itp file the
How can I do that using OPLSAA, because in the nb.itp file the values
are for sigma/epsilon? Can I change C6=0 in the code file?
Quoting David van der Spoel :
On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote:
Hello,
Is there a way to turn off the 6-term in LJ 6-12 potential?
-Nisha P.
On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote:
Hello,
Is there a way to turn off the 6-term in LJ 6-12 potential?
-Nisha P.
Set the parameters to zero?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden.
Questions inline...
On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Tuesday, August 31, 2010 2:45
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users
>
> >
> > Tha
- Original Message -
From: Sai Pooja
Date: Tuesday, August 31, 2010 2:45
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users
>
> Thanks Mark. I have just 2 more queries regarding this. > > When using
> tables for the potential, &
:54 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Monday, August 30, 2010 3:33
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users
>
> > Hi,
> >
>
> > I am simulating a system of a prot
- Original Message -
From: Sai Pooja
Date: Monday, August 30, 2010 3:33
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users
> Hi, >
> I am simulating a system of a protein in water. I am trying to run the
> simulation with a modified protein-
Hi,
I am simulating a system of a protein in water. I am trying to run the
simulation with a modified protein-water LJ and coulomb interaction. Since
LJ and coulomb interaction parameters are defined at the atomic level in
the forcefield files, I cannot figure out a good way to modify them for
pr
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Hash: SHA1
On 08/24/2010 02:27 PM, Sai Pooja wrote:
> Hi,
>
> If there are n types of atoms in protein, how does one specify:
> 1) Different types of LJ non-bonded interactions for different pairs?
> 2) Modified Coloumb(by a pre-multiplier) interactions for diff
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