[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/27/12 10:00 AM, Bala S wrote:
>
>> Anirban,
>>
>> Exactly.. That's the gap (either side of the leaflets) I was mentioning
>> about. I'll try EM and check itagain.
>>
>>
> EM won't fill in solvent gaps.  If you're using my protocol for increasing
> the C radius in vdwradii.dat, then a small gap is normal and will close
> when doing equilibration as the solvent fills in around the lipid
> headgroups.
>
>  Yes, as Justin mentioned, the equilibration runs (restraining the
protein) will fill those gaps.

Anirban

-Justin
>
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> ==============================**==========
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> Justin A. Lemkul
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> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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