Thanks for your reply and suggestions.
On Thu, May 2, 2013 at 8:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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> >>> <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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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> >>> <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<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
