[gmx-users] Query in protein insertion in membrane

[Priya Das]

Sir, ideally what should be the scaling factor. I used 0.75 and i saw that
area per lipid is decreasing profoundly.
Is it ideal to do more rounds of iteration with higher scaling factor say
0.95
On Dec 4, 2014 8:09 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 12/3/14 9:29 PM, Priya Das wrote:
>
>> Dear Sir,
>> Yes it is a large protein. Should i increase the cut off radius or should
>> i
>> decrease the scaling factor to acheive a good insertion.
>>
>
> I have no idea what you mean by "achieve a good insertion."  At this
> point, all that's happened is precisely what you should expect.  You have a
> big protein that overlaps a bunch of lipids.  Those lipids got deleted.
> What is the issue?
>
> -Justin
>
>  On Dec 4, 2014 3:20 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 12/3/14 7:21 AM, Priya Das wrote:
>>>
>>>  Dear All,
>>>>
>>>> i have inserted protein in infalted lipid bilayer. (512 lipids)
>>>> I need to delete almost 100 lipids.
>>>> So should i reduce the scaling factor or increase the cutoff radius in
>>>> this
>>>> command.
>>>>
>>>>
>>>>  Why is that a problem?  Presumably you just have a very large protein.
>>>
>>> -Justin
>>>
>>>   perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>>>
>>>>
>>>>
>>>>
>>>>  --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
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>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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