Thanks very much to the folk who did all the hard work on GROMACS.
Yesterday I did a simulation of the nuclear receptor VDR for 1 nanosecond,
and, using Vega-ZZ for analysis, was able to identify the entrance tunnel
for the ligand. This is something I have been trying to do for several
years... Kudos to the GROMACS team!... The next step is to show the ligand
enter and migrate to the binding pocket.
I have already used Autodock 3 to identify a number of moderate affinity
ligand binding sites adjacent to the ligand entry tunnel. Several of these
look likely to induce ligand entry in an MD simulation, so I am needing to
figure out how to get the computing equipment together capable of running
50 nsec or so of simulation (I think 50nsec, do you agree with this estimate?)
At the moment I am using an overclocked E4300 Core 2 Duo (the just-released
Intel chip). With a 4 ps step I don't get torsional violations, and I can
simulate one nanosecond every 3.2 hours of time on just one half of the CPU.
But I would like to get both halves of the CPU doing the calculation, and
am having trouble with the compilation switches to achieve that. I have an
SMP Linux kernel (v2.6.19) which allocates multiple jobs nicely between the
cores (for example, when I am running twelve single-threaded Autodock jobs
simultaneously, everything works fine) but when I tried to compile the FFTW
and GROMACS sources (with gcc 4.1) the Configure script complains that this
compiler doesn't recognize the MPI commands.
Is it possible to compile using gcc 4.1 so that I get an SMP system using
both cores of my CPU? Do I need a different compiler? What switches or
script tweaks do I need?
Sincerely
Trevor
------------------------------------------
Trevor G Marshall, PhD
Dept of Biological Sciences and Biotechnology, Murdoch University, Western
Australia
Director, Autoimmunity Research Foundation, Thousand Oaks, California
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