[CP2K:1866] Re: methane in a water box with FIST

[Teodoro Laino]

This is not possible (NPT ensemble supports only as possible thermostats 
NOSE and CVSR).
I agree with you that LANGEVIN is just another kind of thermostat and 
should stay between the
other thermostats. But it was developed as a different ensemble.. maybe 
one day it will disappear
and reappear between the thermostats.. For the time being  I would 
recommend you for this case
the CSVR . It's quite effective (have a look at the original paper).


Teo


Marius Retegan wrote:
> 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
>>>>>
>>>>>
>>>>>           
>>     
>
> >
>