[gmx-users] entropy calculation

[pooja_gupta at nccs.res.in]

thank justin
>
>
> On 7/17/13 8:19 AM, pooja_gupta at nccs.res.in wrote:
>> i took only single structure
>>>
>
> You can't calculate entropy from a single structure.  Please investigate
> the
> literature.
>
> -Justin
>
>>>
>>> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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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