From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 22 2012 - 04:53:31 CDT
On Wed, Aug 22, 2012 at 11:37 AM, Francesco Pietra
<chiendarret_at_gmail.com> wrote:
> Do you mean that, for instance, parm7 or charmm27, are not for high
> pressure? Otherwise, "physiological conditions" are not only at
i suppose that was the intent. the approximations that
lead to classical force fields can be seen a "mean field"
approach and thus they have limited transferability to
conditions they were not parameterized for.
this applies to conditions like temperature or pressure,
but also density and composition (i.e. choice of solvent).
the interesting question here always is *how much*
that limitation applies to certain condition and what
kind of accuracy do you expect overall. people already
often have inflated expectations on force field accuracy,
when moving to different conditions, the errors incurred
are getting even larger. however, that doesn't keep
people from doing those calculations, and considering
the limitations, they can still be useful (when looking
at trends instead of absolute numbers and generally
not overinterpreting data).
> 300K/1bar. Think to deep-sea organisms: if they were internally at
> such conditions, they would be simply squeezed.
force fields don't care about these things. ;)
they are just numbers.
axel.
>
> chiendarret
>
> On Wed, Aug 22, 2012 at 10:05 AM, Jernej Zidar <jernej.zidar_at_gmail.com> wrote:
>> Dear Sir,
>> Doing simulations at such high pressure doesn't make any
>> (bio)physical sense as these conditions are really far from the
>> physiological conditions.
>>
>> Best,
>> Jernej
>>
>> On Wed, Aug 22, 2012 at 4:02 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>> Hi all:
>>>
>>> I was scanning - with little success - NAMD mailing list for
>>> equilibration of water-solvated proteins at relatively high pressure,
>>> say 100 bar and 285K.
>>>
>>> Any experience, in particular to the best flags for such conditions?
>>> What about the pressure fluctuation due to the scarce compressibility
>>> of the medium under such conditions?
>>>
>>> thanks
>>>
>>> francesco pietra
>>>
>>
>>
>>
>> --
>> Windows: Re-Boot, Linux: Be-Root.
>>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:56 CST