Re: [gmx-users] Extracting temperature of specific groups during the simulations
On 3/25/20 11:40 AM, Mijiddorj B wrote: 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 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 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? Google is your friend... https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090607.html -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.
Re: [gmx-users] Extracting temperature of specific groups during the simulations
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 > 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 > 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.
Re: [gmx-users] Extracting temperature of specific groups during the simulations
On 3/25/20 8:40 AM, Alessandra Villa wrote: HI, On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B 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. -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.
Re: [gmx-users] Extracting temperature of specific groups during the simulations
HI, On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B 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. Best regards Alessandra > Best regards, > > Mijiddorj > -- > 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. > -- 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.
