From: Ana Celia Vila Verde (acavilaverde_at_gmail.com)
Date: Fri Apr 18 2014 - 02:12:40 CDT
Hi Francesco,
Hmm, there's nothing in principle wrong with this behavior. If you're
unsure, why don't you start 10 runs and see where your protein goes in
each case? I would guess that your protein will sometimes stay in the
middle of the box and sometimes will move.
Ana
On 4/18/14 12:02 AM, 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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