[gmx-users] Temperature for individual amino acid residues

[Justin Lemkul]

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 ?
>

I guess that 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.

-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-**March/004870.html<http://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html>
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> 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>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>

-- 
========================================

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

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