[gmx-users] entropy calculation

[Justin Lemkul]

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

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