[gmx-users] Query in protein insertion in membrane

[Justin Lemkul]

On 12/3/14 9:43 PM, Priya Das wrote:
> 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

Yes, 0.95 is best for most cases.  If you scale too quickly, the lipids will not 
relax well enough.

-Justin

> 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
>>>>
>>>> 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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>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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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

==================================================