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

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/27/12 6:40 AM, Bala S wrote:
>
>> Thanks for the reply.
>>
>> I'm following the tutorial.
>>
>>
> Please clarify whether you're using Anirban's or mine.  Now that two
> exist, people will have to be a fair bit more specific :)
>
>
>  In your system, to solvate it you have the values that was used during the
>> protien insertion into the bilayer. Following it, I have used the
>> following
>> commandfor my system where the protein is very much smaller than the
>> length
>> of the bilayer.
>>
>> $ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350
>> 6.59650
>>
>> $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top
>>
>>
> If you have to manipulate the box of any coordinate file produced by
> InflateGRO, whatever you're doing is wrong.  You should not be solvating
> anything until the very last step of the procedure, where your bilayer is
> of correct size and APL.


Exactly, solvate at the end of all the compression steps performed by
InflateGro (may be 10 or 20 depending on your system) and minimizations (of
only protein + lipid)  until you have reached the correct area per lipid.
And then only solvate. Check for the dimensions in the last line of the
FINAL (compressed and minimized) .gro file and then solvate

Thanks,

Anirban

>
>
>  But I could see in the visualizer that SOL molecules were added on top and
>> bottom but only 1/3 of the length of the bilayer.
>> How to add SOL molecules to whole length or how to remove not-solvated
>> part
>> of lipids?
>>
>>
> This outcome is a consequence of re-adjusting the box size of a system
> that likely has other dimensions.  As far as I can tell, you shouldn't be
> doing this.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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