Dear Justin and Alessandra, Thank you very much for your prompt response. I saved both velocity and energy data in every 1 ps.
> ------------------------------ > > Message: 5 > Date: Wed, 25 Mar 2020 08:43:46 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Extracting temperature of specific groups > during the simulations > Message-ID: <167bcf35-f905-9c66-a9d6-e1799132d...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 3/25/20 8:40 AM, Alessandra Villa wrote: > > HI, > > > > On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B <b.mijidd...@gmail.com> > wrote: > > > >> Dear GMX users, > >> > >> I would like to extract the temperatures for specific groups during the > >> simulations. gmx energy gives the system temperature as a function of > time. > >> I also tried to get the temperature of a specific group using gmx traj. > >> However, the data of gmx traj much lower values of the system > temperatures > >> for any groups in the systems. I also tried to extract GROUP.tpr and > >> GROUP.trr files from original data. Then, I performed rerun for the > group. > >> However, these data is more lower than that the data of gmx traj. > >> > >> I have two questions if possible please advise me. > >> 1. Is it possible to make correction for the data of gmx traj? > > 2. Are there any other methods for this purpose? > >> > > The values you get by gmx traj are calculated on the number of frames > that > > you have saved in trj file (assuming that you have saved velocities in > your > > trajectory file). If you have saved with different frequency the energy > and > > trj files, you may get different temperature values since you are > > calculated the temperature on different set of data. > > When you performed a rerun, you have to be sure that you save every step > > (that you have in your original trajectory) in the new generated energy > > file. Otherwise also here you will end up to calculate the temperature > on a > > different set of data. > > > > Accounting for these points, you should get comparable results with the > > different approaches. > > The saving interval will only account for a very small difference, one > that will likely be within the error estimate. The biggest difference in > the outputs of gmx energy and gmx traj is that gmx traj has no knowledge > of constraints, so it computes degrees of freedom incorrectly. One can > recover the proper temperature by scaling the output of gmx traj after > computing the correct number of (unconstrained) degrees of freedom. > Thank you again. I am sorry for further asking. Can you briefly guide me to compute the correct degrees of freedom? How can I scaling the output? Best regards, Mijiddorj > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 191, Issue 59 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
