On 10/05/2012 7:29 PM, Debayan Chakraborty wrote:
Dear Gromacs Users,
I want to simulate an organic dye in
a solvent ( such as aniline as DMA). I have already relaxed the
solvent around the dye in the equilibration run ( NPT) using position
restraints on the
On 5/9/12 10:37 PM, DeChang Li wrote:
Dear all,
I want to calculate the ion solvation free energy (e.g. an ion
Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR)
method, following the tutorial by Justin A. Lemkul. However, if I turn
off the Coulombic interaction, the
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On Sat, May 5, 2012 at 7:27 PM, Za Pour za.p...@yahoo.com wrote:
Dear gmx users
I am simulation a system including carbon nanotube+water.I have done these
things:
However as I looked into the nvt.gro I realized that the cylindrical shape
of carbon nanotube
has been changed.I am not sure
Dear gromacs users,
I performed a Hemiltonian Replica Exchange (i.e. replica exchange where
each replica has a init_lambda=0, delta_lambda=0 and init_lambda ranging
uniformely from 0 to 1).
Since I have only ten fixed discrete lambda, I run a Temperature Replica
Exchange where, for each replica
4.6 will include Hamiltonian replia exchange functionality built into
the MPI version.
Currently the description of the error is very vague -- if you can
write up what exactly the numbers are, and what they should be, with
files that exactly replicate the error, then I can take a look. But
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