Re: NAMD with infinite cutoffs?

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Jun 04 2019 - 08:49:36 CDT

That might be true, but to my knowledge "PME off" is a completely different
code path from "GBIS on". In any event, I don't think what you are
describing has been intentionally implemented, at least not for any serious
application. The nearest I can think of is MSM, but I've never had time to
play with that code.

On Tue, Jun 4, 2019 at 9:41 AM Norman Geist <norman.geist_at_uni-greifswald.de>
wrote:

> But it does actually work, at least without GBSA. The only problem is with
> the cutoffs that need to be smaller than the box.
>
>
>
> Thank you
>
> Norman Geist
>
>
>
> *Von:* Brian Radak [mailto:brian.radak_at_gmail.com]
> *Gesendet:* Dienstag, 4. Juni 2019 14:59
> *An:* namd-l <namd-l_at_ks.uiuc.edu>; Geist, Norman <
> norman.geist_at_uni-greifswald.de>
> *Cc:* Vermaas, Joshua <joshua.vermaas_at_nrel.gov>
> *Betreff:* Re: namd-l: NAMD with infinite cutoffs?
>
>
>
> 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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