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] Average rmsd
Ok i ll try Thanks On Mon, 29 Apr 2019, 7:06 am Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hi Neelam, > > I do not have Xmgrace tool, but you can open up the xvg file on excel and > calculate average. > -- > 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] Average rmsd
Hi Neelam, I do not have Xmgrace tool, but you can open up the xvg file on excel and calculate average. -- 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] RMSD command line doubt
Hello gromacs users, My goal is to calculate all-atom rmsd of every structure in the trajectory(.trr) to the final structure after simulation (.gro). Q1) So, I don't understand the purpose of giving .tpr input file (which was the input structure file before production mdrun) as a structure file in the command. gmx rms -f peptide.trr -s peptide.tpr -o rmsd.xvg Q2) When I use final structure .gro file (after production mdrun), I get the following warning: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. Please let me know if I am misunderstanding here anything. Many thanks, Neena -- 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] Assertion failed: Condition: ic->coulomb_modifier == eintmodEXACTCUTOFF
Hi, I am using Gromacs 2018.6 to run a simulation of dppc lipids and the input file is as follows. 26 cutoff-scheme = Verlet 27 verlet-buffer-tolerance = -1; set rlist manually 28 nstlist = 10 29 ns-type = grid 30 pbc = xyz 31 rlist = 1.4 ; nm 32 33 coulombtype = Reaction-Field-zero 34 epsilon-rf = 035 epsilon-r = 15 36 rcoulomb-switch = 0 37 rcoulomb= 1.2 38 39 vdwtype = Cut-off 40 vdw-modifier= Potential-switch 41 rvdw-switch = 0.9 42 rvdw= 1.2 43 DispCorr= no I successfully got tpr file but failed in mdrun command. The error is as follows, Program: gmx mdrun, version 2018.6 Source file: src/gromacs/mdlib/forcerec.cpp (line 2653) Function:void init_forcerec(_IO_FILE *, const gmx::MDLogger &, t_forcerec *, t_fcdata *, const t_inputrec *, const gmx_mtop_t *, const t_commrec *, float (*)[3], const char *, const char *, const t_filenm *, const gmx_hw_info_t &, const gmx_device_info_t *, int, float) Assertion failed: Condition: ic->coulomb_modifier == eintmodEXACTCUTOFF With the group scheme RF-zero needs the exact cut-off modifier Best Regards, Kangxin LIU -- 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.
