[gmx-users] lipid molecules are overlapping with proteinmolecule

[Padmani Sandhu]

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..???



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
>
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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*