On 5/20/12 2:30 AM, jrustad wrote:
Justin A. Lemkul wrote
You don't need the pull code if the two atoms are in the same
[moleculetype] - a
molecule in Gromacs is any set of atoms; they don't necessarily have to
make
chemical sense. The only problem I see is that if you have two atoms in
Thanks- yes, I suspected this might be the case, however, in the context of a
free energy calculation it seems difficult to associate the lookup table
with a molecule type rather than an atom type. In other words, I have
defined a molecule Fe which will change from Fe2 to Fe3.
So, its true
On 5/19/12 1:13 PM, jrustad wrote:
Thanks- yes, I suspected this might be the case, however, in the context of a
free energy calculation it seems difficult to associate the lookup table
with a molecule type rather than an atom type. In other words, I have
defined a molecule Fe which will
Justin A. Lemkul wrote
I don't know how complex the system is you're dealing with, but at this
point,
isn't it just far more straightforward to construct a rudimentary force
field
with a few atom types rather than rely on (slow) tabulated functions and
potential funny business to get
On 5/19/12 5:42 PM, jrustad wrote:
Justin A. Lemkul wrote
I don't know how complex the system is you're dealing with, but at this
point,
isn't it just far more straightforward to construct a rudimentary force
field
with a few atom types rather than rely on (slow) tabulated functions and
Justin A. Lemkul wrote
You don't need the pull code if the two atoms are in the same
[moleculetype] - a
molecule in Gromacs is any set of atoms; they don't necessarily have to
make
chemical sense. The only problem I see is that if you have two atoms in
the
same location, while
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