Re: [gmx-users] Replica exchange MD analysis
RajP, For future questions, if you don't get a response, then change the question, add further details etc. Repeating the same question several times doesn't improve your chances of getting a response. Your question is very broad, general and lacks specifics, hence why no one has responded. Show that you've done some work, tried things, used existing resources, etc. No one is here to do your research for you. Questions to ask yourself : Why are you performing REMD? What property or properties will provide insight into that? What analysis can you perform to gain insight into the behaviour of those properties? What is published in the same/similar area? What analysis, scripts and software have you tried? What exactly are you having difficulty with? "I am not able to get the analysis part" doesn't really tell us anything. On Sun, 24 Mar. 2019, 8:51 pm Rituraj Purohit, wrote: > Dear Friends, > I performed REMD by following tutorial provided by Mark Abraham, But I > am not able to get the analysis part. Is a step-wise tutorial > available ? I would be thankful to you if anyone of you could help me > to perform analysis of REMD output. Thanking you > Regards > RajP > -- > 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] Question about gmx order ...
First guess would be the atom at which the property is being calculated i.e. radial line from the COM through the atom. On Sat, 23 Mar. 2019, 6:43 am Sergio Garay, wrote: > Hi all > > I have a micelle trajectory formed by 30 molecules, and I would like to > obtain the order parameters of each acyl chain moieties. I've tried using > the option -radial, but I'm not sure about the result. What will be the > director that it will be used in the calculation? It will be a vector from > the center of mass to.what? the tool is not asking for any terminal > atom to calculate the end of the director. Probably I'm wrong, but I'm not > sure how to continue. > Any help will be very appreciated! > > Sergio > -- > 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] Grompp error
Hello everyone I am using gromacs version 2019, and I want to add dihedral restraint to the backbone of the last helix in my protein in my simulation, however grompp gives me this error ERROR 1 [file D2-TorisionRes.itp, line 5]: Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. (after the function type). from my understanding this means that i am missing one feild in my restraint file, can someone tell me what is it?This is the content of my D2-TorisionRes.itp file :[ dihedral_restraints ] ;For the second domain starting from residue 74 ; ai aj ak al type label phi dphi kfac power ; C(i-1) Ni C-alphai Ci 1 1 value 0 1.0 2.0 1159 1174 1175 1176 1 1 -70.2 0 1.0 2.0 ;res 74 1176 1186 1187 1188 1 1 -91.0 0 1.0 2.0 ;res 75 1188 1205 1206 1207 1 1 -53.4 0 1.0 2.0 ;res 76 and in my topology file i added this line after the molecule:; Include Dihedral restraint file #ifdef DIHRE #include "D2-TorisionRes.itp" #endif and in my mdp file i used:define = -DDIHRE is my implementation of the dihedral restraint correct so far? also do i have to include them in all the equiliberation steps? THank you for the help Sent from my iPhone -- 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] Replica exchange MD analysis
Dear Friends, I performed REMD by following tutorial provided by Mark Abraham, But I am not able to get the analysis part. Is a step-wise tutorial available ? I would be thankful to you if anyone of you could help me to perform analysis of REMD output. Thanking you Regards RajP -- 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] Cannot find position restraint file
Hi Neena, The position restraint file is a bit of a new concept. It's the "positions/coordinates" around which the restraints should be applied. That means your posre.itp file was found and requires now the coordinates around which to apply the restraints. Most often people will use their initial system as the "reference" coordinates for the restraints: gmx grompp ... -c em.gro ... -r em.gro Mat On Sun, Mar 24, 2019 at 3:39 AM Neena Susan Eappen < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > For the equilibration phase 1, an error message came up following this > command: > > gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr > Error: Cannot find position restraint file restraint.gro (option -r) > > I do not have a posre.gro file, only posre.itp file. I don't understand > this, any insight would be appreciated. > > Thank you, > 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. > -- 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.
