Oh yes - that makes a lot of sense! Once again, thanks for both of your help.
Will
Sent from my iPhone
> On 29 Jan 2015, at 13:49, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Thu, 2015-01-29 at 12:32 +0000, William Hester wrote:
>> Hi Ross,
>>
>> You are correct, the minimisation/ heating was run at NVT and then NPT
>> for the MD. I am inexperienced in biological simulations and haven’t
>> heard of formation vacuum bubbles before. Is there any specific reason
>> for this, during the building of the system for example?
>
> Yes :). If you hold the volume fixed, and that volume is too large,
> then the external pressure that leads to those conditions must be *very*
> low. Basically, your simulation is boiling.
>
>> I specified the PBC by opening the system in VMD and using the
>> minimax measurement which makes me wonder if the membrane wasn’t
>> sufficiently tightly around the protein?
>
> minmax overestimates the box size. Not horribly, but it does. NPT is
> really the best way to get the "correct" box size for standard
> conditions.
>>
>> I checked the XST file during the MD and sure enough the cell
>> dimensions converge to a value of about 5A less in each direction so I
>> have restarted the simulations and no separations! Thank you so much
>> for the help - I’ve been stuck on this for a couple of weeks now!
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri Jan 30 2015 - 04:00:02 PST
