methane in a water box with FIST

Axel akoh... at
Thu Mar 12 17:03:08 UTC 2009

On Mar 12, 11:39 am, Teodoro Laino <teodor... at> wrote:
> 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).


two comments.

if i understood the CSVR algorithm correctly, it is actually
not very different from using langevin dynamics with a small friction
coefficient (which is what people using NAMD typically do, for

as for "wrapping" coordinates back into the principle unit cell.
check out:

pbc wrap -orthorhombic -compound res -all

should do what people usually expect, and fairly efficient, too.

please note, pbctools have seen some significant improvements and
bugfixes and you may need to download a VMD alpha test version
(they are actually not _that_ experimental currently) to get a version
that is consistent with the online documentation (and has lots of
other interesting goodies. ;-) ).


> Teo
> Marius Retegan wrote:
> > On Thu, Mar 12, 2009 at 4:19 PM, Teodoro Laino <teodor... at> 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> 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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