[gmx-users] entropy calculation

[pooja_gupta at nccs.res.in]

i took only single structure
>
>
> On 7/17/13 8:09 AM, pooja_gupta at nccs.res.in wrote:
>> okk
>>
>> This may be very basic question.
>> I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I
>> picked up one unfolded structure from the trj and solvated with water. I
>> ran em for full system. now i am calculating the entropy. I afraid if i
>> missed something.
>>
>
> Are you running g_covar on the original 10 ns trajectory, or on a single
> energy-minimized structure?  That latter would not make sense.
>
>> I am doing this first time.
>
> There is a large body of literature on configurational entropy related to
> the
> quasiharmonic approximation.  I would suggest you look into its underlying
> theory and how others apply it to biomolecular simulations.
>
> -Justin
>
>>>
>>> On 7/17/13 7:56 AM, pooja_gupta at nccs.res.in wrote:
>>>> I used system (0) for g-covar.
>>>>
>>>
>>> Most likely, g_anaeig is running out of memory.  Try using some subset
>>> of
>>> the
>>> system, like the protein only or its backbone.
>>>
>>> -Justin
>>>
>>>>> On 7/17/13 7:42 AM, pooja_gupta at nccs.res.in wrote:
>>>>>> thanks for reply
>>>>>>
>>>>>> i am using Gromacs 4.5.5 version
>>>>>> command
>>>>>> g_anaeig -v *.trr -entropy  -s *.tpr -extr -f *.pdb -rmsf -3d -comp
>>>>>>
>>>>>
>>>>> What was the g_covar command used to generate the eigenvector .trr
>>>>> file?
>>>>> What
>>>>> group did you choose for analysis during g_covar?
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 601
>>>>> 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.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> 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.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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-- 
Pooja Gupta, Ph.D.
DBT-RA, Lab of Structural Biology
National Centre for Cell Science
NCCS Complex,University of Pune Campus
Ganeshkhind, Pune 411007
India
Email: pooja_gupta at nccs.res.in/ poojagupta.135 at gmail.com
Phone: +91-20-25708158