AW: NAMD with infinite cutoffs?

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jun 04 2019 - 08:40:09 CDT

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 PBCs.

 

On Tue, Jun 4, 2019 at 1:00 AM Geist, Norman <norman.geist_at_uni-greifswald.de <mailto: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 <mailto: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 <mailto: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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