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 <jalem...@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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Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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