Re: [gmx-users] Question about scaling

2012-11-12 Thread Carsten Kutzner
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.

[gmx-users] Question about scaling

2012-11-12 Thread Thomas Schlesier
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

Re: [gmx-users] Question about scaling charges

2006-09-01 Thread David Mobley
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

[gmx-users] Question about scaling charges

2006-08-31 Thread Arthur Roberts
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