[gmx-users] Is anyone also using lammps?s
r.friedman at bioc.uzh.ch
Wed Nov 4 15:45:01 CET 2009
AFAIK GMX only uses fftw for PME.
If you have no reason to prefer flexible bonds you can use LINCS or
SHAKE to constrain the bond lengths and run with a timestep of 2fs at
You may want to try LAMMPS and GMX with SHAKE and a timestep of 2fs and
see if the results are similar before recompiling GMX. If I understood
you correctly you didn't constrain the bonds.
Peng Yi wrote:
> Hi, Ran,
> Do you mean the simulation I used here for testing purpose? That is
> not long, maybe a few hours. But my research will require simulations
> for days. If I will not use PME, do I still need a fftw?
> On Wed, 4 Nov 2009, Ran Friedman wrote:
>> Hi Peng,
>> It would be slower - never made any benchmarks on how much slower. But
>> you don't run a very long simulation, do you?
>> Installing it isn't a problem. If you use PME you also need fftw in
>> double precision though.
>> Peng Yi wrote:
>>> Hi, Ran,
>>> No, I haven't. I still have to find out how to install in double
>>> precision. Would double precision be slower than single? If so,
>>> how much? Or just double the memory used? Thanks,
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