[gmx-users] Temperature for individual amino acid residues

bipin singh bipinelmat at gmail.com
Thu May 2 16:28:43 CEST 2013

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.
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) ?
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 ?

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
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
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Thanks and Regards,
Bipin Singh*

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