From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Apr 18 2014 - 03:14:49 CDT
Hi Ana:
No, the protein moves after a relativelylarge number of steps. Now, I have
taken the last conformation and I'll go to pFS again.
francesco
On Fri, Apr 18, 2014 at 9:12 AM, Ana Celia Vila Verde <
acavilaverde_at_gmail.com> wrote:
> 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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