Hi Thomas,
On Nov 12, 2012, at 5:18 PM, Thomas Schlesier wrote:
> Dear all,
> i did some scaling tests for a cluster and i'm a little bit clueless about
> the results.
> So first the setup:
>
> Cluster:
> Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR
> GROMACS version: 4.0.7 and 4.5.
Dear all,
i did some scaling tests for a cluster and i'm a little bit clueless
about the results.
So first the setup:
Cluster:
Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR
GROMACS version: 4.0.7 and 4.5.5
Compiler: GCC 4.7.0
MPI: Intel MPI 4.0.3.008
FFT-library: ACML 5.1.0 fma4
Arthur,
You might want to start by reading something basic on how force fields
work, i.e. in Leach's Molecular Modeling book, or maybe Jay Ponder's
recent "Force Fields for Protein Simulation" review (available on his
web page here: ftp://dasher.wustl.edu/pub/papers/advprotchem-66-27-03.pdf).
I
Hi, all,
I was talking to a friend of mine that works in
an MD lab. He said that the charges from QM/MM or
semiempirical need to be scaled to charges in the
force field. For example, a heme will have specific
charges in the force field, while hemes that represent
different bound states may
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