[CP2K:1864] Re: methane in a water box with FIST

Teodoro Laino teodor... at gmail.com
Thu Mar 12 15:19:59 UTC 2009

Marius Retegan wrote:
> 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?
not possible with CP2K but you can use VMD for that purpose (it's only a 
visualization issue).
> 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?
Sure. It's a different ensamble called LANGEVIN.


> Thanks,
> Marius
> 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
> >

More information about the CP2K-user mailing list