[CP2K:1859] Re: methane in a water box with FIST

Marius Retegan marius.s... at gmail.com
Thu Mar 12 15:18:42 UTC 2009

Hi Teo,

Thanks for the quick fix (as usual). After the first NVE simulation
with PBC I've visualize the resulting trajectory with VMD. As expected
some of the water molecules "diffused" into the neighboring boxes. Is
it possible to get from cp2k a re-imaged trajectory?
>From what I've seen in the manual in the case of a NVT simulation, two
options exist for controlling the temperature: NOSE and CSVR. In the
past I've also used a Langevin thermostat for this purpose. I this
possible with cp2k?


On Wed, Mar 11, 2009 at 7:10 PM, Teodoro Laino <teodor... at gmail.com> wrote:
> Hi Marius,
> thanks for reporting this problem. The bug is now fixed in the CVS.
> Cheers,
> Teo
> Marius Retegan wrote:
>> Hello
>> I have some problems running a simulation of methane in a TIP3P water
>> box. I've added the input, coordinates and amber parameter file to
>> repository (mebox.tar.gz). I think that the problem is related to the
>> fact that some of the LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF have
>> zero value, which gives NaN for the van der Waals parameters in the
>> case of hydrogen atoms. Also I would like to add that the simulation
>> work fine with Amber8.
>> Thanks
>> Marius
>> >
> >

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