one question about solvent dynamics seen in the npt production run
initially using octahedral cell. During visualization by VMD I've seen
water spreading in all dimensions with significant increasing of the box
size (looks like no pbs have been applied). From tutorial I've found
possible re-imaging script using cpptraj after which my system looks like
in the fixed box size. Does such system increasing is some artifact? How
I could measure pbc box vectors during md ?
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
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 10 2014 - 03:00:02 PDT
