Re: implicit solvent

From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Mar 27 2013 - 12:30:09 CDT

ahh right. If you do the high cutoff and set staticatomassignment on so
that the pairlists don't need to be regenerated, would the two be
equivalent? I guess it still makes more sense to use the fullDirect method
rather than assuming you'll always be under your arbitrary cutoff.

On Wed, Mar 27, 2013 at 1:26 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:

> When PME is not available, rather than using 9999 as cutoff there is an
> option fullDirect to compute all electrostatic pair terms explicitly.
>
>
>
> On Wed, Mar 27, 2013 at 1:20 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>
>> Also, are you using a GPU?
>>
>> And, are you intending to set the cutoff to something approximately
>> infinite (9999 or somesuch)? Keep in mind that with implicit solvent you
>> no longer have the ability to use PME, so if any nonbonded interactions get
>> cutoff, it could be problematic, though it might not matter that much
>> depending on what you are doing.
>>
>>
>> On Wed, Mar 27, 2013 at 12:31 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>>
>>> On Wed, Mar 27, 2013 at 5:27 PM, Fugui <theoreticalchem_at_163.com> wrote:
>>> > Dear NAMD users:
>>> > I will do an implicit solvent MD using NAMD, can anyone tell me the
>>> speed of
>>> > the implicit solvent MD compared to explicit solvent MD. I have a
>>> protein of
>>> > 300 amino acids.
>>>
>>> it will be faster.
>>>
>>> axel.
>>>
>>> > BW
>>> > Fugui
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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