Re: peptide tends to migrate out the water box

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Apr 18 2014 - 10:27:09 CDT

Assuming you know how Periodic Boundary Conditions work, what makes you
think this is a problem?

On 04/17/2014 06:02 PM, Francesco Pietra wrote:
> During accelerated MD (boost on dihedral) in TIP3wader periodic box with
> namd2.9_CUDA, the peptide is folding correctly, albeit still at an
> incomplete stage. However, after barely 500,000 steps ts=2fs, the peptide
> has gradually migrated toward a face of the box.
>
> I never observed before such a behavior for a box built with "padding 15",
> i.e., with plenty of water around the peptide under non-CUDA accelMD for
> these types of peptides.Flags that might be relevant to the phenomenon
> observed:
>
>
> rigidBonds all ; # needed for 2fs/step
> # rigidBonds water
> rigidTolerance 0.000001
> exclude scaled1-4
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 13.5 ;# cutoff +3.5
> margin 0
> 1-4scaling 1.0
> PME yes
>
> wrapNearest no
> wrapAll on
>
> Thanks for advice.
>
> francesco pietra

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