David and all,
> Sorry, my brain was on vacation (about the N). Anyway, having C2 as VS
> would mean the molecule remains perfectly linear as it should be, and
> you do not have to define angles of 180 degrees which gives you an
> ill-defined force.
Isn't there a robust implementation that wouldn
David Mobley wrote:
David,
On 10/16/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
David Mobley wrote:
All,
I may be in a hole of my own digging, here, but I've been trying to
simulate a large set of small molecules in explicit solvent. I'm using
the Amber GAFF parameters, converted over
David,
On 10/16/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> David Mobley wrote:
> > All,
> >
> > I may be in a hole of my own digging, here, but I've been trying to
> > simulate a large set of small molecules in explicit solvent. I'm using
> > the Amber GAFF parameters, converted over to
David Mobley wrote:
All,
I may be in a hole of my own digging, here, but I've been trying to
simulate a large set of small molecules in explicit solvent. I'm using
the Amber GAFF parameters, converted over to GROMACS using our
amb2gmx.pl script.
The problem I'm running into is that for anything
All,
I may be in a hole of my own digging, here, but I've been trying to
simulate a large set of small molecules in explicit solvent. I'm using
the Amber GAFF parameters, converted over to GROMACS using our
amb2gmx.pl script.
The problem I'm running into is that for anything with a triple bond
(i
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