[gmx-users] lipid molecules are overlapping with proteinmolecule

[Padmani Sandhu]

The main problem is that energy of the system does not reach to a minimum
value, it get stuck at a single atom and a constant energy value for all
steps. Does "-DSTRONG_POSRES" applied to the protein may cause a
problem..??? You have mentioned to apply position restraints to heavy atoms
of protein, does that mean the whole protein..??

On Wed, Nov 12, 2014 at 6:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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> 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
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>>> University of Maryland, Baltimore
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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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-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*