[gmx-users] Decreasing of the box size during membrane protein simulation

[James Starlight]

Justin,

yes, 2 A for C atoms.

The dims are 8.68740   8.41864  10.00000


James

2013/1/28 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 1/28/13 8:30 AM, James Starlight wrote:
>>
>> Justin,
>>
>> Below you can see graph representation of my system after energy
>> minimisation ( that case system was filled up with tip3p water using
>> genbox  with slightly increased vdw for C atom ( to 2nm) to prevent
>
>
> I'm assuming you mean 2 Angstrom?
>
>
>> water movement into the membrane.
>>
>> http://img42.imageshack.us/img42/7213/b2armembrane.png
>>
>
> I can't exactly guess what the dimensions of the system are, but it seems to
> me that the z-dimension is not 10 nm based on a rough guess of how many
> lipids are present.
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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