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

[Teodoro Laino]

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.

Cheers
Teo

> 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
>>>
>>>       
>>     
>
> >
>