[gmx-users] lipid molecules are overlapping with proteinmolecule
jalemkul at vt.edu
Wed Nov 12 13:47:39 CET 2014
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
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.
> 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 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
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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
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