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 <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 > > -- > ==============================**========== > > 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@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-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *----------------------- Thanks and Regards, Bipin Singh* -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
