Hi,
On Tue, Jun 10, 2014 at 3:36 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> in the fixed box size. Does such system increasing is some artifact? How
> I could measure pbc box vectors during md ?
FYI you can extract the unit cell vectors with cpptraj and the
'vector' action with the 'ucellx'/'ucelly'/'ucellz' keywords, e.g.
vector ux ucellx out ucell.dat
etc
You can get the box lengths with the 'box' keyword for 'vector'.
-Dan
>
>
> James
>
>
> 2014-06-09 22:13 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
>
>> Many thanks!
>>
>> James
>>
>>
>> 2014-06-09 19:39 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>>
>> On Mon, Jun 9, 2014 at 10:59 AM, James Starlight <jmsstarlight.gmail.com>
>>> wrote:
>>>
>>> > Jason,
>>> >
>>> > thanks for suggestions. Could you also tell me 1) may I use initial
>>> heating
>>> > of my system in NPT (not NVT) which could prevent such density
>>> fluctuations
>>> > during this stage using appropriate pressure coupling constant?
>>>
>>>
>>> Probably. Depends on the other settings. I typically heat over ~100 ps
>>> with restraints on the solute using NVT and then switch to NPT to
>>> stabilize
>>> the density. But I've also used NPT to heat before without adverse
>>> consequences. You should inspect your trajectory if you are unsure
>>> whether
>>> there are problems or not.
>>>
>>> However, heating with NPT will not lessen how much the unit cell will
>>> shrink. The only thing that it will help with is preventing the formation
>>> of bubbles if you see bubbles begin to form during your heating stage.
>>>
>>> 2) What
>>> > problems might be occurred during simulation in octahedral boxes?
>>> >
>>>
>>> Truncated octahedrons don't support anisotropic scaling (at least in
>>> Amber). However, it typically doesn't matter what shape periodic cell you
>>> use. [1]
>>>
>>> HTH,
>>> Jason
>>>
>>> [1] Except when it does matter, like for crystal simulations (that need to
>>> use the same shape box as the asymmetric unit cell) or instances where
>>> anisotropic pressure control is required, like for surfaces and layers
>>> (that typically require an orthorhombic box).
>>>
>>> --
>>> Jason M. Swails
>>> BioMaPS,
>>> Rutgers University
>>> Postdoctoral Researcher
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jun 10 2014 - 08:00:02 PDT
