Re: [gmx-users] SASA calculation for one replica in REMD
The trajectory output from GROMACS is specific to that specific ensemble, in your case at given temperature. So each individual trajectory is for a given temperature. And that sounds like it is exactly what you want. If you want to follow the trajectory for a single replica, that's when it gets a little more complicated and you need to use the demux script and some further processing. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 29 Apr 2019 at 13:56, Shan Jayasinghe wrote: > > Dear Gromacs Users, > > Thank you for all suggestions. Yes I can use gmx SASA, but I want to know > how do we use that in REMD simulations? > > Specifically, I want to calculate SASA for molecules in my first replica > (298 K). But I think the trajectory in the first replica contains the > information regarding to temperature exchanges. However, I want to > calculate SASA for specifically at 298 K. How can we extract information > only for 298 K. > > Thank you for any help that you can provide. > > > > On Tue, Apr 23, 2019 at 7:38 PM Tasneem Kausar > wrote: > > > Check gmx sasa -h > > It is implemented in Gromacs > > > > On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe < > > shanjayasinghe2...@gmail.com> wrote: > > > > > Dear Gromacs Users, > > > > > > I did replica exchange molecular dynamics simulation which contains 25 > > > replicas. Now I want to calculate the solvent accessible surface area of > > > the surfactant (the first replica in my REMD) I used in my simulation at > > > 298 K. How can I do that? > > > > > > Can anyone help me? > > > > > > Thank you. > > > -- > > > 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. > > > > > -- > Best Regards > Shan Jayasinghe > -- > 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.
Re: [gmx-users] SASA calculation for one replica in REMD
Dear Gromacs Users, Thank you for all suggestions. Yes I can use gmx SASA, but I want to know how do we use that in REMD simulations? Specifically, I want to calculate SASA for molecules in my first replica (298 K). But I think the trajectory in the first replica contains the information regarding to temperature exchanges. However, I want to calculate SASA for specifically at 298 K. How can we extract information only for 298 K. Thank you for any help that you can provide. On Tue, Apr 23, 2019 at 7:38 PM Tasneem Kausar wrote: > Check gmx sasa -h > It is implemented in Gromacs > > On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > Dear Gromacs Users, > > > > I did replica exchange molecular dynamics simulation which contains 25 > > replicas. Now I want to calculate the solvent accessible surface area of > > the surfactant (the first replica in my REMD) I used in my simulation at > > 298 K. How can I do that? > > > > Can anyone help me? > > > > Thank you. > > -- > > 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. > -- Best Regards Shan Jayasinghe -- 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] SASA calculation for one replica in REMD
Check gmx sasa -h It is implemented in Gromacs On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > > I did replica exchange molecular dynamics simulation which contains 25 > replicas. Now I want to calculate the solvent accessible surface area of > the surfactant (the first replica in my REMD) I used in my simulation at > 298 K. How can I do that? > > Can anyone help me? > > Thank you. > -- > 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.
Re: [gmx-users] SASA calculation for one replica in REMD
Hi, I don't know if sasa calculations are implemented in gromacs. But if you know a little bit of Python you can use MDTraj for that: http://mdtraj.org/latest/examples/solvent-accessible-surface-area.html or also Pymol: https://pymolwiki.org/index.php/Get_Area Cheers, Simone Il mar 23 apr 2019, 11:07 Shan Jayasinghe ha scritto: > Dear Gromacs Users, > > I did replica exchange molecular dynamics simulation which contains 25 > replicas. Now I want to calculate the solvent accessible surface area of > the surfactant (the first replica in my REMD) I used in my simulation at > 298 K. How can I do that? > > Can anyone help me? > > Thank you. > -- > 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.
[gmx-users] SASA calculation for one replica in REMD
Dear Gromacs Users, I did replica exchange molecular dynamics simulation which contains 25 replicas. Now I want to calculate the solvent accessible surface area of the surfactant (the first replica in my REMD) I used in my simulation at 298 K. How can I do that? Can anyone help me? Thank you. -- 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.
