[gmx-users] lipid molecules are overlapping with proteinmolecule

[Justin Lemkul]

On 11/11/14 10:18 PM, Padmani Sandhu wrote:
> hello justin,
>
> Energy minimization is not converging to Fmax in 20000 steps in between
> shrinking steps. I tried it for 50000 steps also, What can I do to resolve
> it..???
>

Whether or not that matters depends on what you have set as emtol.  You need to 
provide the actual output, but if you are getting large forces, you probably 
built the system wrong or invoked InflateGRO incorrectly.  After the initial 
inflation and deletion of lipids, if you properly do energy minimization, there 
should never be atomic overlap.

-Justin

>
>
> Regards,
>
> Padmani
>
> On Tue, Nov 11, 2014 at 6:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
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>>
>> On 11/11/14 6:45 AM, Padmani Sandhu wrote:
>>
>>> Hello all,
>>>
>>>
>>> I am trying to energy minimize a trimeric protein in DPPC bilayer but
>>> facing problem in reaching desired lipid per area using "inflategro.pl".
>>> After 5 or 6 steps of shrinking and energy minimization lipids molecules
>>> start interfering with protein. I tried to increase cutt-off, but that is
>>> also giving error during grompp.
>>>
>>>
>> Proper energy minimization between shrinking steps should eliminate this.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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

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