[gmx-users] Unstable system [was: (no subject)]

[Justin Lemkul]

On 10/15/14 10:56 PM, Padmani Sandhu wrote:
> I have also carried out MD simulation for the same comlex in water and that
> worked perfectly.
>

Then the problem is in how you have assembled the bilayer system, but it is 
impossible to say what it is at this point.

-Justin

> On Thu, Oct 16, 2014 at 1:50 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
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>> On 10/15/14 12:35 PM, Padmani Sandhu wrote:
>>
>>> Hello Justin,
>>>
>>>
>>>
>>> Epot = -3.4264112e+07
>>> Fmax= 8.5767386e+02
>>> from energy minimization.
>>>
>>>
>> Seems reasonable.
>>
>>   I am using force field Gromos43a1 and ligand parameters were derived from
>>> PRODRG.
>>>
>>
>> PRODRG produces topologies full of errors.  Have you done any manual
>> adjustments to improve the quality of the topology?
>>
>>   I have also minimized same protein-ligand complex in the water ealier.
>>>
>>>
>> So minimization works, but does an MD simulation work?  That will help
>> sort out whether or not the issue is related to the membrane.
>>
>> -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

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