[gmx-users] Temperature for individual amino acid residues

[bipin singh]

Thanks for your reply and suggestions.


On Thu, May 2, 2013 at 8:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/2/13 10:28 AM, bipin singh wrote:
>
>> Thanks for the reply.
>> I have seen the link. As given in the link that we need to multiply the
>> temperature by (3N-Ncons)/3N. Please let me know if I have correctly
>> interpret context of the statement. "N" is the total number of protein
>> atoms and "Ncons" will be equal to total number of constrains.
>>
>
> N = number of atoms in the group being analyzed
> Ncons = number of constraints in that same group
>
>  1) Do we have to take total numbers of "pairs" mentioned in .top file as a
>> "Ncons" ( I am using all-bonds constraints in mdp file) ?
>>
>
> Pairs have nothing to do with degrees of freedom.
>
>  2) So, do we need to multiply by this value (single uniform number for all
>> residues) to temperature at each step of every residue in a protein ?
>>
>>
> There is no single value; each group analyzed will have its own scaling
> factor.  Use of the scaling factor depends on what you want to observe, but
> multiplying each frame's value by a constant and then averaging gives the
> same as averaging and multiplying by a constant, so you might save yourself
> some work if you just care about averages.
>
> -Justin
>
>
>>
>> On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 5/2/13 1:54 AM, bipin singh wrote:
>>>
>>>  Hi All,
>>>>
>>>> I want to calculate temperature for each individual amino acids residues
>>>> present in a protein after the simulation. I know that this can be done
>>>> with help of g_traj, but my concern is whether this will give me correct
>>>> temperature or not because it was mentioned that g_traj
>>>> does not mind the constraints. Please let me know what type of
>>>> correction
>>>> need to done on the output from g_traj if we need correct temperature
>>>> values.
>>>> OR
>>>> Is there any way to get it from .edr file...
>>>>
>>>>
>>>>  http://lists.gromacs.org/****pipermail/gmx-users/2003-****
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>>>
>>> -Justin
>>>
>>> --
>>> ==============================****==========
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
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>>
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
*-----------------------
Thanks and Regards,
Bipin Singh*