Re: [gmx-users] Vibrational spectra of amide I using gromacs
Dear Andre, Thank you very much for your kind responses. According to your suggestion, I calculated the bond length as a function of time. The auto-correlation function was generated by gmx analyze. Then, I used the xmgrace for the Fourier transform of the Auto-correlation function. Is the workflow right? The result data does not look like some spectra. How can I convert it into vibrational spectra and how can I adjust the unit? If possible, please advise me? Thank you again for your time. Best regards, Mijiddorj > -- > > Message: 6 > Date: Wed, 8 Jan 2020 22:33:56 -0300 > From: Andr? Farias de Moura > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Vibrational spectra of amide I using gromacs > Message-ID: > < > caktwkgrecyh10wma+sw_86rhyop9c6k2xspknvyoewiufky...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Mijiddorj, > > It is a matter of taste, but I like to use xmgrace for that kind of > analysis. > > The GROMACS tool gmx analyze can do that for you: > http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html > > Andre > > On Wed, Jan 8, 2020 at 9:18 PM Mijiddorj B wrote: > > > Dear Andre > > > > Thank you very much for your quick response. > > I am very new for this type of analysis, and I would like to ask > further. I > > am sorry for that. Is there any good software? > > If you have any experience, please suggest me some useful software for > the > > time series correlation and the Fourier transformation. > > > > Best regards, > > > > Mijiddorj > > > > Should be doable using any standard spreadsheet: > > > > > > (1) save the bond lengths along the simulation for the bond of interest > > > > > > (2) compute the time correlation function for these bond lengths (the > > > autocorrelation function for this time series) > > > > > > (3) compute the Fourier transform of the time correlation function > > > > > > Andre > > > > > > On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B > > wrote: > > > > > > > Dear gmx users, > > > > > > > > Hello, I would like to ask vibrational spectra of amide of specific > > > > amino acids. Is it possible to analyze from classic MD calculations > of > > > > gromacs? > > > > Or > > > > > > > > Is there any software that is compatible with gmx trajectories to > > > > calculate the spectra? > > > > > > > > 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. > > > > > > > > > > > > > -- > > > _ > > > > > > Prof. Dr. Andr? Farias de Moura > > > Department of Chemistry > > > Federal University of S?o Carlos > > > S?o Carlos - Brazil > > > phone: +55-16-3351-8090 > > > > > > > > > -- > > > > > > > > > > > -- > > 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. > > > > > -- > _ > > Prof. Dr. Andr? Farias de Moura > Department of Chemistry > Federal University of S?o Carlos > S?o Carlos - Brazil > phone: +55-16-3351-8090 > > > -- > > -- > 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 189, Issue 19 > ** > -- 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] Vibrational spectra of amide I using gromacs
Dear Mijiddorj, It is a matter of taste, but I like to use xmgrace for that kind of analysis. The GROMACS tool gmx analyze can do that for you: http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html Andre On Wed, Jan 8, 2020 at 9:18 PM Mijiddorj B wrote: > Dear Andre > > Thank you very much for your quick response. > I am very new for this type of analysis, and I would like to ask further. I > am sorry for that. Is there any good software? > If you have any experience, please suggest me some useful software for the > time series correlation and the Fourier transformation. > > Best regards, > > Mijiddorj > > Should be doable using any standard spreadsheet: > > > > (1) save the bond lengths along the simulation for the bond of interest > > > > (2) compute the time correlation function for these bond lengths (the > > autocorrelation function for this time series) > > > > (3) compute the Fourier transform of the time correlation function > > > > Andre > > > > On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B > wrote: > > > > > Dear gmx users, > > > > > > Hello, I would like to ask vibrational spectra of amide of specific > > > amino acids. Is it possible to analyze from classic MD calculations of > > > gromacs? > > > Or > > > > > > Is there any software that is compatible with gmx trajectories to > > > calculate the spectra? > > > > > > 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. > > > > > > > > > -- > > _ > > > > Prof. Dr. Andr? Farias de Moura > > Department of Chemistry > > Federal University of S?o Carlos > > S?o Carlos - Brazil > > phone: +55-16-3351-8090 > > > > > > -- > > > > > > > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Vibrational spectra of amide I using gromacs
Dear Andre Thank you very much for your quick response. I am very new for this type of analysis, and I would like to ask further. I am sorry for that. Is there any good software? If you have any experience, please suggest me some useful software for the time series correlation and the Fourier transformation. Best regards, Mijiddorj Should be doable using any standard spreadsheet: > > (1) save the bond lengths along the simulation for the bond of interest > > (2) compute the time correlation function for these bond lengths (the > autocorrelation function for this time series) > > (3) compute the Fourier transform of the time correlation function > > Andre > > On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B wrote: > > > Dear gmx users, > > > > Hello, I would like to ask vibrational spectra of amide of specific > > amino acids. Is it possible to analyze from classic MD calculations of > > gromacs? > > Or > > > > Is there any software that is compatible with gmx trajectories to > > calculate the spectra? > > > > 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. > > > > > -- > _ > > Prof. Dr. Andr? Farias de Moura > Department of Chemistry > Federal University of S?o Carlos > S?o Carlos - Brazil > phone: +55-16-3351-8090 > > > -- > > > -- 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] Vibrational spectra of amide I using gromacs
Should be doable using any standard spreadsheet: (1) save the bond lengths along the simulation for the bond of interest (2) compute the time correlation function for these bond lengths (the autocorrelation function for this time series) (3) compute the Fourier transform of the time correlation function Andre On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B wrote: > Dear gmx users, > > Hello, I would like to ask vibrational spectra of amide of specific > amino acids. Is it possible to analyze from classic MD calculations of > gromacs? > Or > > Is there any software that is compatible with gmx trajectories to > calculate the spectra? > > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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.
