From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 27 2013 - 12:26:15 CDT
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
>
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