[gmx-users] Is anyone also using lammps?s

[Ran Friedman]

Hi Peng,

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
room temperature.

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.

Ran

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?
>
> -Peng
>
> 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.
>>
>> Ran
>>
>> 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,
>>>
>>> -Peng
>>
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