From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Jun 04 2019 - 07:59:19 CDT
Unfortunately NAMD's implicit solvent implementation is not meant to work
with PBC*s.*
On Tue, Jun 4, 2019 at 1:00 AM Geist, Norman <norman.geist_at_uni-greifswald.de>
wrote:
> Hey Joshua, exactly, the system should be periodic and with normal
> cutoffs, there exist spots within the cell where two solutes don't fully
> see each other.
>
>
> Am Dienstag, den 04-06-2019 um 00:01 schrieb Vermaas, Joshua:
>
> Hi Norman,
>
> Why not just make your cutoffs unimaginably large and run without periodic
> boundary conditions? Is there some part of your system that to be
> replicated to infinity.
>
> -Josh
>
>
>
> On 2019-06-03 14:51:22-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hey Brian, thanks for your suggestion, however the fulldirect thing wont
> work for me since I have implicit solvent conditions.
>
> Best wishes
> Norman Geist
>
>
> Am Montag, den 03-06-2019 um 20:21 schrieb Brian Radak:
>
> Look for the "FullDirect" keyword in the user guide and note all of the
> caveats.
> HTH,
> BKR
>
> On Mon, Jun 3, 2019 at 12:32 PM Geist, Norman <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> Hey there,
>>
>> is there a possibility to have infinite cutoffs in NAMD. More
>> specifically, is there a way to consider all interactions without running
>> into problems with cutoffs to close to the box size?
>>
>> Regards
>> Norman Geist
>>
>
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