[gmx-users] entropy calculation

[pooja_gupta at nccs.res.in]

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.

I am doing this first time.

Pooja
>
>
> 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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