[CP2K:1865] Re: methane in a water box with FIST

[Marius Retegan]

On Thu, Mar 12, 2009 at 4:19 PM, Teodoro Laino <teodor... at gmail.com> wrote:
>
> 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.

OK. How about adding pressure control while still regulating the
temperature with a Langevin thermostat?

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