[gmx-users] Temperature for individual amino acid residues

Justin Lemkul jalemkul at vt.edu
Thu May 2 16:39:05 CEST 2013

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.


> 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>
>> ==============================**==========
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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


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